It does suck, it really does - I too was very worried about the antibiotic - and they thought I would have to be on it for the remainder of my pregnancy...luckily I was given the all-clear by the urologist after a month, but I still worry about the affects of the abx on baby in utero. My midwife seems to think the probiotic therapy should help rememdy at least some of the effects though - so I'm glad about that.
She (MW) also had me take vit c, uva ursi (some say not rec. in pregnancy - but my case was severe enough she felt benefits outweighed drawbacks) and I'm still taking cranberry capsules.
Watch that lower back pain - that is where I started the day I was hospitalized....I'm a homebirther, natural pregnancy kind of person - and I ended up with four days of narcotics. Take GOOD care of yourself and rest, so that you can take good care of your baby too....