Our puppy had a bladder infection soon after we got her, so we got the wee-wee pads for her just for that. Normally I would not use them, I prefer that she go outside, but she was just going to pee in the house anyways because she couldn't hold it in so I figured these would help the cleanup. They didn't work for me, she peed everywhere else but on them, and like someone else said, she tried to chew them, but who knows, your puppy might use them properly.
I don't think it'll start any bad habits because she's sick and she's going to do it on your floor anyways. Just go back to taking her outside when she's feeling better, and I'm sure it won't be much of a setback for you. It wasn't for us.