lots of people get freaked out about medications. they almost look for issues that could possibly be connected to meds.
my daughter,, when she was 9 to 10 yrs old, was on 500mg of amoxicillin 3X a day for SIX months to treat Lyme disease. she is fine. Being she was on them for a long time, the big thing we looked for was stomach issues. so we made sure she took probiotics and I had her eat yogurt.
the deal is meds are necessary. they sometimes have annoying side effects. However what is the alternative? Not take a prescribed medicine and allow an infection (in your case) to take over and make worse problems? In my daughter's case, was I supposed to let Lyme disease ruin her because I was afraid of potential side effects of the amoxicillin?
IMO--if you have an infection that your doctor felt needed anti-b's, not taking them opens you up to bigger issues than being tired and having a headache (which, truthfully could still be a product of anxious thinking----self fulfilling prophecy). Don't let your fear make decisions for you. In the end, of course, it is up to you.