From all that I have seen here through the years, Pentasa is just not a potent enough drug to treat CD long term. He may actually get more symptom relief and healing from the metronidazole (Flagyl). However, 6mp is becoming more and more a primary drug of choice in CD treatment for inducing and sustaining long term remission, or at least moderation of symptoms, and it seems to be well tolerated by most patients. Do keep in mind that it takes 3-6 months for 6mp to reach full effectiveness. In some cases, GIs will combine 6mp and steroids until the 6mp kicks in.
If he is having frequent episodes of bleeding, that is a strong indication that he is still having raw ulcerations in his colon, which would be a sign that his current medications are not holding the line.
You'll find lots of personal stories on here re the various drugs used to treat Crohn's, and especially about how this disease is different for every patient. It is also important to keep in mind that posts on this forum tend to reflect the worst sometimes . . . not every Crohn's patient has to have surgery or has major life-altering symptoms. Lots of CD patients live generally healthy, productive lives, but they are probably less likely to post on sites like this one. Be grateful that his disease has been diagnosed at a fairly young age . . . time was, not that long ago, that a lot of us had to go 10-20 years with active disease, often diagnosed as irritable bowel or just "nerves", before the true diagnosis could be made. Scopes and other modern technology have done a lot, and there are always new drug therapies emerging.
The 6mp dosage used for Crohn's is far lower than that used in cancer treatment (primarily for leukemia.) There have been a number of studies done of long term 6mp usage for Crohn's that show no appreciable increase in cancers . . . and in fact, the primary risk of developing bowel cancer in Crohn 's is uncontrolled inflammation. While some people do report side effects from 6mp, they are a small minority (I think the rates run under 5%) and those effects can be easily reversed by simply stopping medication.
You may want to see how the flagyl does . . . I was on it after diagnosis for some time and it did a fairly good job of controlling my disease, but results from 6mp have been better, with no side effects.
One thing to keep in mind with Crohn's is that there are two or three new drugs developed every year these days. I would not be surprised if by the time your son reaches his 30s there is a whole new arsenal of treatments out there, and that 6mp and Pentasa and even Remicade have been relegated to the scrap heap.
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.