Quick Answer:
Some doctors are fine with letting patients be on lower doses of prednisone for years, while some doctors are more conservative. I have talked to a crohn's patient from this forum who has crohn's and asthma, and is on prednisone at varying doses (probably 10-40mg). He has been on pred since he was younger (maybe 12 y/o), he is now about 23 and is still taking pred. I believe he did report taking Fosamax now, to assist with osteoporosis...which is very unfortunate for someone his age. Chances are you may find a doctor ok with this, but if you DO start to head down this road, it is usually advisible to take calcium supplements, to help your bones out. Also, many folks consider taking Entocort if they really don't wanna step away from using steroids. Entocort is usually only effective for the terminal ileum and ascending colon, however, so that may not be whats best for you, and you may well only get by with the more systemic prednisone.
A few things to consider...your GI may have you try methotrexate injections...which is in the same class of drugs as 6mp or Imuran, but by taking it subcutaneously, doesn't usually cause as much stomach upset etc. So there are a few other meds out there to try, without going to the biologics like remicade etc.
Side Note: prednisone should also be helpful for your arthritis...but may further upset your GERD