I'm afraid I cannot offer an easy fix. I can think of various ways I can make something like this safer in the long term, but they don't help you now.
If you can afford a couple of days down time, I would probably use a rescue CD and do it all off-line. I would probably still use a separate USB drive as that would stop the main array drives from seeking to update the backup file. If you cannot afford that, just wait.
I could possibly 'fix' mdadm so that it is possible to kill it and restart it, but I can't make any promises about when that will happen. I'll let you know if I do end up with something I trust though.