This is a really tricky one tbh. My twin boys are both autistic. One is severely so (DS1), and with profound learning disabilities. They initially shared a room until they were about 3 when DS1 would hit DS2, take his covers, and once smeared faeces on him. Clearly this wasn't fair on DS1, but as we lived in a 2 bed flat, my only option was to give up my room and sleep in the living room. They are both 12 now and we have a 3 bed house. DS1 doesn't cope very well with other children, and needs his own space to retreat to when he gets overwhelmed and disregulated.
Was their father aware of this when it was decided they would share a room at your house? If so, how was he planning on dealing with it? Did he really think it was a good idea?
That being said, his ex was out of order to pretty much say you shouldn't have had your son and to make the demands she has. I do understand her concerns, as one of her daughters is regularly being hurt by her sister and it seems that her father isn't taking any steps to prevent it.
I don't think it would be fair to turf your son out of his room. Personally i would give up my room for the 2 nights the girls stayed, but I do understand that this is something that many people wouldn't contemplate, and that's fair enough.
I don't think having one girl sleep on a sofa bed downstairs is a solution either. Assuming they go to bed much earlier than you do, it would mean you would lose the use of that room in the evenings. Plus, and I don't know if this is all children or just mine, but mine would hate to be downstairs alone in the middle of the night. And which girl do you pick? Can the autistic girl be trusted to be alone downstairs in the middle of the night? It isn't her own space either which would make her feel disregulated. If her sister sleeps downstairs on the sofa bed instead of in a comfy bed in a nice bedroom, it will feel like she's being punished because her sister hits her. If you alternate, it will probably cause the autistic girl to become disregulated by things changing.
Is it possible to divide the girl's room? That seems like the only thing that would make sense. But it would need to be properly divided to stop DSD attacking her sister.
Don't have either girl sharing with your son. It's not fair on him. Clearly autistic DSD can't share with him, and other DSD will again feel like it's unfair and she's being punished.
As for some of the total shit some commenters are spouting on here, I would like to add:
No, my sons don't need a separate house. DS1 will attack DS2, or try to, but DS2 can either escape up to his room to safety, but generally I intervene first because I can see when it's about to happen. In the middle of the night when I was asleep in my room and they were in their room, I couldn't see what was going on to be able to prevent it.
Holidays aren't really something we can easily do. We occasionally have a caravan holiday, and yes, I do have to pay for the boys to have their own rooms. A hotel is not an option for us. But for other holidays, they still need to have their own rooms.
I don't know if it will be the same for DSD, but DS1 is becoming more aggressive as puberty kicks in. So don't think it's something she may grow out of soon.
So while I don't think you need to necessarily follow what their mum has suggested, you do have to do something. "Addressing the behaviour" takes time, and DSD will continue to get hurt during this time, and it isn't fair on her to not take immediate action.
(I suspect their mum won't like the idea of one girl going over at a time as it means she loses her childfree time!)