You're not at all unreasonable about the shoes off rule.
However, this is batshit:
Not even sure how I will tackle the 'please would you mind washing your hands before holding the baby'. Too frightened to even go there... I think my DH family all think I am crazy. My friends and family on my side think I am being reasonable though.
You need to work on your OCD tendencies. The baby is going to present many challenges for you unless you get on top of this, and your anxieties are going to have a negative effect on the baby if left untreated.
Too frightened to even go there...
You need to 'go there' and grapple with this.
Wrt the shoes, I like the idea of offering her a choice of either slippers or shoe covers.
You are going to have to deal with what the rest of the IL family think and say about you. Stick to your guns. Develop a thick skin.
Maybe deal with your anxiety about how others react in a therapeutic setting, if it is keeping you up at night. You seem to be in the grip of quite a lot of anxiety, over lots of issues.
Is it possible your MIL has picked up on your OCD tendencies and is trying in a clumsy, blunt force way to force you to confront them?
Same goes for your ILs?
Keeping the house pristine for the sake of the baby is misguided and I personally would roll my eyes at that because you are simply wrong about exposure to dirt and germs.
If you have talked with these people about your preoccupation with germs in the context of the baby then I suspect they are trying to teach you something. They are right in what they are trying to teach you, if that's what they are doing, but not right in the way they are going about it.
Keeping new, light coloured carpets clean as long as possible is a valid concern however (imo).
Though it might have been smart to choose a colour that is a little darker, given the fact that a baby-toddler-small child will be living in the home, but you live and learn.
(Speaking as a mother of 5 who bought a couch that was upholstered in cream...)