We switched to anti-bacterial hand soap and found that just doing regular cleaning was more important than which particular cleaning product we used. Even vinegar can be a pretty good antiseptic since it inhibits bacterial growth. Washing our hands frequently was probably most important of all. You can find some tips about avoiding mold at
WebMD. I suggest keeping your daughter from getting into household plants you might have in planter pots, and keeping her away from people who are sick as much as possible. I don't think it's necessary, or possible, to maintain an immaculate environment, and just trying to keep a reasonably clean and safe house is a good goal.
With a 2-year-old you have to worry more about what's on the floor and what she's putting in her mouth than about kitchen or bathroom counters. You can't achieve perfection with a toddler; germs are always going to be a part of their world and little ones just naturally get into everything! But sweeping and vacuuming will give her a cleaner environment. Some families leave their shoes off in the house since shoes tend to track in a lot of dirt.
I'm just guessing, but her pacifier might keep her from putting other things in her mouth, meaning it might actually be a benefit. Of course, she'll probably drop it on the floor now and then, pick it up, and put it back in her mouth, but that's probably still better than having her hands in her mouth all the time.