I 2 box with a tank and healer for pve and I get the same problem. I have a key setup to auto follow, and another key setup to turn left so the healer will stop autofollowing and hang back and heal. 99% of the time it works but then there's the %1 of the time when, for no reason that I can fathom, the healer just won't stop and runs straight for the mobs.

The only workaround I have is to be aware that this will happen once in a while (it's not that often really although it sucks when it does happen) and to quickly tab over to the healers window and STOP the toon.