Sorry to hear about your son's diagnosis. More and more GI's are using the "top down" approach - using the "bigger" drugs first in an effort to get the disease under control quickly. This is a great presentation about the risks and benefits of drugs used for IBD:
http://programs.rmei.com/CCFA139VL/
My daughter is on both Remicade and MTX. Initially, the decision to put her on biologics was very hard, but after seeing the difference they made to her quality of life, we have never looked back. I can honestly say that we've never regretted that decision for a second. Yes, the drugs are scary but the disease is much scarier. Researchers are also finding that the cancer risk is less than previously thought.
As for a needle phobia, the sad truth is most kids learn to deal with needles relatively quickly. Most Children's Hospitals have Child Life Specialists available who can help. There are also things you can use - Emla cream or Buzzy:
http://buzzy4shots.com
Good luck and hang in there! The first few months are the most overwhelming.