It used to be that GIs prescribed Flagyl for extended periods in CD, but the practice now is to use is for a briefer period -- weeks instead of months -- to induce remission and then to go with other drugs for long term therapy. So the two refills you quote are about right.
While there is a confirmed genetic link to Crohn's disease, it is not so strong that it clearly runs in families, like cystic fibrosis or some forms of cancer. So just because you have no close relatives with CD, that does not exempt your son. I suspect if you did a poll you'd find that most folks on here have no familial pattern.
The biopsies taken during a colonoscopy look for several things, among them granulomas, to help confirm the Crohn's diagnosis. However, those markers only show up in a minority of biopsies. The diagnosis is based on clinical picture -- symptoms over time, exam -- and appearance of the colon and terminal ileum in the scope. The number one sign is ulcerations and skip areas of inflammation. Also keep in mind that your son is fairly young and has probably not yet developed some of the pathologies that would show definiitively on biopsy. He is, however, right at the age when a very large percentage of CD patients begin to show symptoms and receive their diagnosis. I think you can accept this diagnosis with some confidence. There's a reason for chronic GI problems and bleeding over time, and that reason is usually Crohn's when the scope confirms it.
You have also been urged to avoid falling in love with the MAP and other trendy theories, which is good advice. It really doesn't matter what causes a runaway immune system reaction like Crohn's (or arthritis or lupus or MS). What matters is what you do to treat the synptoms and minimize the damage once that process has been identified.