Yes, it's overwhelming at first, but it does get easier once you get a good long-term treatment plan in place. I'm another one who wishes we had started biologics earlier. My daughter wasn't diagnosed until last year, at age 12, but she had had symptoms since she was 7. As a result of being untreated for so long, she had fistulizing disease, which led to scarring that has probably caused strictures. She's still doing very well right now, but she has to be careful about what she eats, and I wish we'd been able to start treatment earlier.
Like your son, my daughter always got extremely worked up by blood draws, so I also was not thrilled with the idea of the Remicade infusion. I won't lie to you--it's still not easy for her--but we've found ways to make it bearable. First, we always put lidocaine cream on her arm about an hour before the IV goes in. We also just started using a Buzzy (buzzyhelps.com) while the IV is placed, and that helps too. She plays games and watches videos on an iPad during the infusion itself, and I also bring some of her favorite foods along. Finally, we used a small dose of Ativan (lorazepam) for the first few infusions, because she was really anxious beforehand, even in the car on the way to the hospital. She doesn't need the Ativan any more.
There are also kids on the forum who've successfully gone to see a therapist about their needle phobia, so that's another option.
One nice thing about Remicade is that all blood draws can be done during the IV placement, so no need for separate blood draws for labs.
Good luck with your decision-making. I know it's not easy.