I don't think it was ever a question of the Mercs duking it out or not. It was all about insulating Hamilton from Vettel's attack.
According to a Hamilton interview (so you can take it with a grain of salt), he didn't ask for the re-order, and he didn't want it. Apparently over the radio he said, "Just ask him (Bottas) to speed up a bit"
I can actually live with the re-order in that scenario - it's almost the same as the Force Indias swapping position to each have a go at attacking Magnussen - just in a defensive sense rather than offense. I just would have preferred for them to revert to their original positions before the end of the race once the threat from Ferrari was gone. (But I grasp why they didn't)
It's no different from:
Kimi, Sebastian is faster than you.
Fernando is faster than you.