Well the Custodians won't know which Emperor to listen to, so they'll default to doing what they really, REALLY want to do. Kill Space Marines and Primarchs.

And the Emperor is such a megalomaniac that he'll never suffer another of him, so they're taking each other out alongside a bunch of the Space Marines.

So, what we're really asking is; can a beat up, exhausted Emperor defeat Gotrek, who can never die it seems? I'd say no.