C.R.
Well I've lived in a home for the past 11 years on hardwoods. Sounds like you should have chose different flooring, something not porous. Your cleaning them too much and causing damage to them. Getting hardwoods wet is always a bad idea. If you have to do it only do it on occasion not regularly.
You should have another baby, that will break you of being so "cootie" paranoid problem ")
Sorry I'm not much help about disinfecting your floors. I suppose if I did anything I would go with the vinegar and water route as someone else suggested. Spray lightly and mop up quickly. You'll want to use something natural as chemicals are not good for baby to be crawling around on.
Best Regards,
C.