You're not stupid, you just didn't understand how the system worked. That's where they let you down. They're probably more used to dealing with people who have been in various systems all their lives and already know how things work. But you didn't know anything and they should have explained. That's why I'm trying to explain it all to you now, so you'll know for next time.
Regarding your partner. I think definitely try to get him removed from the house by police. But speak to women's aid about it for their opinion. He says he'll kill you but that doesn't mean he will or even that he'd try, he's trying to scare you. Remember to tell the police all about it though, all the details. And if he is removed, make sure you call them every single time he comes back. It's important for building a record for the council for evidence of why you need somewhere else to live.
It's a very good sign that women's aid phoned you to see about if there was a weekend emergency. You are still in their system then, or they wouldn't have called you about it.
It is very difficult for them with workload when there's a bank holiday because all the work has to be done in 4 days instead of 5 and there will likely be extra emergencies over the weekend. So on Tuesday not only is there one less day that week, there's also extra work. Hopefully your allocated support worker will contact you soon. It sounds like they might be considering alternative accommodation.
Temporary homeless accommodation isn't as safe as a refuge, if the temporary accommodation is a hostel. But the staff there can help you enter and leave safely from your room to the outside world so you can buy food etc. You could get a tenancy support worker too, if they have those in your area. They help you with paying bills, managing debts, filling in forms, making phone calls etc. and they'd come to the hostel to help you probably for an hour once a week.
You might not get put in a hostel though. In my area there's a few flats for homeless, which are given to families or people with serious enough health problems who wouldn't cope so well in a hostel. If there's any available it sounds like you might qualify for a flat. Then it's just like renting a flat anywhere and a housing officer pops in weekly to check how you're doing and that you haven't trashed the place etc. The housing officer can give advice too. You can't stay long term in these flats they're temporary homeless accommodation, so you join the housing list like before and bid for permanent housing properties.
If you get offered any sort of temporary homeless accommodation you have to accept it. It's a one-off offer (for the current circumstances anyway, which is your abusive relationship, you could ask again in the future but not eg next week) and if you say No they consider that you don't want their help and they leave you to yourself.
So you must take any temporary place you're offered, no matter how awful it is. And you must not move out until you have a permanent flat to go to.
If it's a flat you come and go as you please. If it's a hostel you can go out for a while, or even all day every day if you want to, or stay inside, but check what time you have to return at night to not be locked out. If you get locked out you will be on the streets that night and you might lose your place in the hostel. So it's important to avoid this.
After a year if you're still in the temporary place because your bidding in the housing list has been unsuccessful, the council find you a housing association flat themselves and offer it to you without you bidding on it. This is how it is in my area anyway.
When it comes to permanent places I think you can refuse the first two you are offered, if you think it's unsuitable, but then you must accept the third one. If you don't accept the third one you'll be considered to not want their help, discharged from the homeless teams help and left to yourself again. If that happens you will not be able to stay in the temporary place. So always check the consequences of refusing a place before you do so.
In the refuge, I will try to explain things. The thing about checking the rooms in numbered order. This is because when they made an exception for you and did your room first, how they saw it was that it didn't make any difference to your distress, you was still upset. They don't have time to make adjustments for people, unless those adjustments are going to make a difference. It didn't make a difference the first time, so that's why they refused to do it the second time.
I don't know what you did the first time, it sounds like you may have been explosive in your temper or behaviour? This is understandable, given your fears. Unfortunately, you might have broken some rule about how to behave towards staff and that could be why the manager asked you to leave.
Or it might have been nothing to do with that. The manager might have meant you needed to leave by bidding on the housing list properties. She might have thought you hadn't been bidding on purpose, she might not have realised that nobody got you onto the list for ages.
I'm going to mention this next thing not to pressure you but just as an explanation. The reason why some people might have been saying to you about getting help with your mental health is because although you don't want medication, what medication does is help you to keep calm during these very difficult times in a refuge where the system of how it's run feels awful for you. The medication would be a temporary quick-fix solution to help you cope through those months until you're permanently housed, and then you could speak to your doctor about coming off it and the best way to go about that. I'm not saying you need to be medicated, I'm just explaining how it could help you temporarily. Medication is not just for insane people, it is for anyone who isn't coping.
Wanting the workmen to return in a few weeks seems reasonable to you but in reality it wasn't, because of the expense of calling a workman out for just one room. So they needed to do all the rooms on the same day.
The thing about coming into the room if you don't answer is because they can see your mental state and they worry you might hurt yourself. So if you don't answer they have to check. Yes you could just be in the bath or asleep but also you could be seriously hurt and need an ambulance. It is their job to check. If someone died and the authorities said why didn't you call an ambulance, if the staff said "well we thought she was asleep so we didn't check" then they would be in so much trouble for negligence. I realize it feels intrusive and controlling to you, but also they have their job to do. They do have to do these checks.
The waking you up is because for a lot of people it helps them to be in a routine. I'm the same as you, it doesn't help me it just makes me more tired. But they were trying something that works for most people. They were trying it because you're not happy to have an appointment or phone call straight away the second you wake up. So they were trying to prevent that by getting you into a routine where you're awake in the day. It didn't work out for you, I understand that, but they were trying their best.
I hope this info helps you feel better about the situation. I don't think they meant to trick you or lie to you. I think they just didn't explain things in enough detail, so you didn't know what was happening and couldn't make good choices. I hope you understand it all a bit better now.