Yes, it's okay to leave her in the bathroom, esp. since the fleas are freaking you out and you wouldn't want her to take it personally!! It's probably traumatic enough for this poor cat to be in a strange place, then making the rounds about town. And it sounds like her owner may be a bit clueless, to say the least, so the poor cat probably doesn't have the best faith in humans to start with. And even though this is a hassle for you, I am so glad that you are able to help this poor kitty out - can you imagine the torment of those flea bites.....Even if you don't get reimbursed by the owner, you will have done your good deed and you should give yourself a pat on the back for that!!! You are doing the right thing, and sooner or later this good you do will come back to repay you many times over!!
I could go on & on about how I've stuck my neck out on a limb, thinking I was being such a fool, & then, later, even months or years later, whomever I've helped, or someone that knew me because of them, will get to repay me....Trust me - you did the right thing!
-this one's for you!!!