I have same kind of problem especially when picking arps and classical pices like Crossroads movie stuff with alternate picking (16-notes around 130-150). I had a thread a while a go about this. Most agree that picking fast from elbow is not good. However I find it impossible to pick from wrist our fingers but lads on this site have told me that´s it´s easy to change if you give it a chanche. So I have decided to pick my way and if I would feel some pain, I´ll change it. Some players have been pickin´ from elbow for years and are fine. I personally think that risk is bigger to develop a injury in your left hand (if you pick with right) but it´s different from person to person.
I remember a doctor who told me that it depend a lot with your overall health. How often you are sick and how often you get inflamation (this is a swedish word but I hope you get it) ´cause stuff like tendonitis and carpal syndrom is simply inflamations wich can take time to cure.
Pick on man and hope that this sh*it goes around you. That´s what I do and as long as I´m well, I won´t complain.
Dejan S. No speed limit