Hi Sl, et al,
I guess the question hinges on the forthcoming events in the story, and whether the hero's decision now makes subsequent events difficult for the reader to accept - or suspend their disbelief, as I was taught to say it. A couple of posters here have touched on that issue and to me, it is the critical one.
Since you're the writer and haven't asked for ways out of the dilemma, I won't give any, but one that is quite workable springs to mind.
A couple of writers have had their protagonist perform some quite violent events without the reader losing contact with the story - Lee Child in the Jack Reacher novels and Barry Eisler with his Rain series. Both writers have handled the motivations of their characters a little differently, and their morals made quite clear. Have you clearly defined your character's morals and motivations?
One question springs to mind though: if the "more powerful being" cannot interfere in the events on Earth and wants your protagonist acting in his stead (and is obviously directing his actions), does this not count as interference? Presumably your protagonist's powers are a subset of the MPG's?
Cheers,
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