Unfortunately, we waited and it was a mistake.
My son had a resection in January. It was the only area of active Crohn's and everything else was clean so his GI said he wanted to wait until 6 months post-op to do scopes and see how things are going. One month after surgery he had the best labs ever... no inflammation and all the numbers were good, so we decided to just keep him on Pentasa and would discuss maintenance meds again in the summer at the 6 month mark.
In April he caught a cold. It triggered something and he went downhill pretty quickly. Within two weeks he was in a full blown flare and miserable. We just had scopes yesterday which confirmed his horrible lab numbers and he's starting a short course of pred along with Azathiopurine today. So, in total, we made it 3 months before the monster was back.
At the time we really were thinking his Crohn's was of the mild variety and we would be okay waiting 6 months. As alex_chris said, there seems to be two schools of thought on this. DS did not have inflammation prior to surgery so we took the conservative approach, but it backfired on us.
In retrospect what would we have changed? Probably nothing. We really had no reason to and like you, the meds scared me. Maybe request monthly labs to check for inflammation until the 6 month mark, just to be on the safe side? Maybe have scopes at 3 months versus 6 months? Really, there is no harm in that, right?
Here are some links that you might find useful:
http://www.wjgnet.com/1007-9327/11/3971.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1773309/
http://www.medpagetoday.com/Gastroenterology/InflammatoryBowelDisease/12695
http://www.practicalgastro.com/pdf/May11/CollinsArticle.pdf
It's just such a crazy disease. My new motto? Expect the unexpected! Keep us posted.