Welcome, and sorry you have reason to be here. I hope by now you've made your decision and that your dd is doing better.
My dd had been on both injectable and oral mtx, as well as Enbrel. My sister who has arthritis (although not JRA) is on Mtx oral and Enbrel (and has been for 7 years now!) She has never had issues with either drug. Dd on the other hand....had numerous issues, but that's a whole 'nother story.
Good luck to you and your dd.