I have taken bactrim many times, it does work and it caused me no additional problems, but that was before being dx with Crohn's. One doc told me a while back that if you take Cipro for a UTI, you are less likely to get one soon after. At the time I was getting them every 3-6 months. So now I ask for Cipro, and I don't get UTI's nearly as often, maybe once a year. Though I also drink cranberry juice like water! Seriously, I buy huge jugs of it at Sam's Club.
Also if you're in a lot of pain they should give you the analgesic, phenazopyridine, it turns your urine orange but it takes the pain away very quickly--faster than with the antibiotics alone. If you can talk to a nurse he/she should be able to prescribe it for you.