I agree, it's a bug. I'll add the issue to the list of GE bugs that need fixing.
There is one thing that you might try: shuffle the reserve positions in such a way so they don't match the backup positions. I always do that and it seems to have helped.
If it's any help, I had the same behavio(u)r demonstrated in my friendly match today, where a starter came in to replace my PG in the last two minutes:
(http://www.buzzerbeater.com/match/45577487/reportmatch.as...)I will have to try to remember swapping positions on the reserves, although I rarely have big enough blowouts that this situation is encountered (I don't know if I've ever seen it with a difference of less than 40 points).