Don't feel bad for rescuing that poor little mite from the pet shop. I would probably do exactly the same thing and this is precisely why kittens should not be sold in pet shops.
The pet shops play on the fact that the little one's in their *care* are usually below par healthwise and therefor likely to be snapped up by someone who cannot bear to see them in these conditions.
I rescued my last little one from a rescue but I use the term rescue very loosely. It was an independant rescue run from someone's house and the place was absolutely filthy. There were about a dozen kittens all lumped in together in one room with one litter tray. The place stank to high heaven. I hadn't gone prepared to bring a kitty home that day but I left with the only kitten she said could go on his own. No home check, nothing. I didn't even have a carrier to take him in and she was completely unconcerned by this.
It took over a week for the smell of urine to wear off him and I couldn't bath him because he'd been frontlined (he was crawling with fleas).
So....I do understand why you went against what you believe in to rescue that little one. You'd have to have a heart of stone not to.