I've taken antibiotics and it never made my flare any worse...but I also take a good quality probiotic (which I feel is an essential tool for us IBDers) I make sure to take my probiotics at least 2 hours after I'm done taking all my antibiotics for the day.
Since antis can basically wipe out all bacteria in the system (good and bad) leaving your system more vulnerable, the probiotics help replenish and keep balance.
You certainly don't want the infected tooth to get worse, cuz that could be a whole new can of worms to deal with that you don't need.