There IS a distinction between facilities that are handicap reserved (like a parking space) and handicap accessible (like a toilet stall). I think most people, myself included, consider a handicap accessible stall available for use unless someone with special needs is present, in which case they should be given priority for its use.
Sounds like the companion care rooms mentioned here are a little ambiguous, wouldn't the better solution be for the facility to post a sign asking that their use be reserved for people with needs?
I agree the FA sounds inconsiderate, no doubt she thought at 6 a.m. the chances of someone needing that room were minimal, but once she saw/heard otherwise she might have expedited her push-back, so to speak. Sorry to say that in a world with lots of dedicated and polite FA's, there are a very few whose post-9/11 power trips can be annoying.