Colonoscopies are extremely common and safe. It's the only way to view the colon and see what is going on in there. I agree that the prep is the worst part, but it's all worth it!
I'm 25 and I've had a colonoscopy. My father died of colon cancer so I am trying to be very proactive about it. I had an endoscopy done at the same time and it was very easy. The worst thing is the preparation (no eating, clearing your colon with laxitives), but the procedure itself is very very easy.
Any medical procedure or treatment can have the rare complication. This is true for everything from surgery to taking aspirin. So with each treatment both you and your doctor need to weigh up the potential benefits of said procedure. I haven't heard of any secondary infections caused from a colonoscopy. However, my grandma has only weeks left to live because she didn't get a colonoscopy when she was recommended to at 50. Nor did she get it when she started having blood in her stools at 55, or even after she started having bad bloating, nausea, and difficulty going. It took a doctor refusing any treatment for her to do it and they found a tumor the size of a grapefruit. She has fought hard for 4 years, but her 6 months left to live was about 8 months ago. And seeing her in constant pain, unable to stand for several minutes at a time, and even unable to control her bladder is a horrific thing that no one needs to go through. If your doctor thinks you need it, I wouldn't give it a second thought. It's not worth the risk of being ignored and having it grow into something unstoppable.