My husband and kids all have AS. AS is like Crohn's - it needs to be treated to prevent progression and damage. Over time, your SI joints and spine can fuse without treatment. Most rheumatologists use anti-TNFs and the newest research is showing that it prevents progression.
My husband's SI joints are completely fused. His spine is partially fused. He has had many hip replacements because of his AS. My girls both have SI joint damage and both have partially fused SI joints. They also have hip damage and will probably need replacements at some point. This is despite aggressive treatment. AS is not fun!
There are various kinds of arthritis that are associated with Crohn's. The kind that affects the SI joints - axial spondyloarthritis or Ankylosing Spondylitis, flares independently of the IBD. It may or may not respond to the medications used for Crohn's.
CCFA has a good handout that explains the various types of arthritis:
http://www.ccfa.org/assets/pdfs/arthritiscomplications.pdf
I would try to see a rheumatologist as soon as possible.
In the mean time, heat (a heating pad) and ice can help. A TENS unit can also help. Some GI's are ok with patients using Voltaren gel (Voltaren is an NSAID but less is absorbed systemically with the gel) but you do need a prescription for that.
Good luck!