I went and replayed to see mcs reactions for those scenes and to an extent not only through the manipulation there is a sense of background understanding to why mc might feel guilty. For example the changing reactions. Manipulation aside I think it is implies some common sense to why that option understand why mc might remember thus feel guilty. If experiencing hypothermia if possible you need to get out of wet clothing and recommend in first aid to remove them as fast as possible. I think coming from that kind of angle of knowing that its less about clothes and more,, medical emergency paired with the manipulation of Crowe would make a person feel more guilty because in this case it is a life or potential medical harm case not just a 'they changed you into pjs because you seemed uncomfortable sleeping in normal clothes' scenario. I think even if the options don't amount to much in terms of ending having a second option to express discomfort or relent the topic even if feeling guilty can keep that understanding to the manipulation and why mc feels that way while still letting people have that option. Or with food, even if the cooking is still rejected Crowe once again could use the medical 'scare' from yesterday into saying food gives energy which should be needed given you used up a lot yesterday which in turn would likely give mc a reason to 'push back' as an option but eventually result in the same guilt of knowing yeah mc doesn't have many options right now and if they plan to pursue leaving would need food/energy/etc type guilt.
This isn't to say this isn't a perfect solution or what should be done but as of now i kind of understand why there is a push-over nature in the first few days as Crowe does have the leverage over the MC and even if these ideas are expanded to result something like getting upset in the later days rather than at the start they might have an effect of that sort of feeling of being manipulated into giving in. I guess what I'm really trying to say is that even though things don't amount to much right now the guilty feeling and being so easy to give in I think makes sense for MC current outcome given that they were begging to be saved by the end of the prologue and in a sense might feel need to be overly polite/give in to who was their rescuer.