I would not say it is common, but certainly not unheard of. It is getting more common as more and more folks live with the j-pouch for longer and longer periods. It seems to me that you've had a lot of problems post op (if I am remembering correctly), so it sort of makes sense that eventually, somewhere down the line, enough evidence would pile up to point more definitely toward a Crohn's diagnosis. It really could happen to any of us.
Your pouch is in no more danger than it was before the diagnosis change. You might even be in better shape, treatment-wise. That is because there are more treatments approved for Crohn's than UC. Yes, you definitely want to seek something that will replace prednisone, since that should never be considered the long term maintenance drug. You can consider all the UC drugs that you have not tried yet, methotrexate, and then biologics (Remicade, Humira, Cimzia). There are more in the pipeline too.
A number of folks here really got their IBD under control once they were diagnosed with Crohn's and on the right treatment. Humira seems to be the treatment du jour these days. But, sadly, yes, some do wind up having to have an end ileostomy. You'll just have to see how it goes.