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A couple of points:

One is that humanity as a species didn't exist the last time the Necrons were awake, so 'an ancient pact' is extremely unlikely.

Secondly, I'm not positive the Necrons still have access to bio-transference tech, or would be willing to use it if they did. This, of course, you're completely able to refluff, especially given how Necrons are spread out across the galaxy and can't really call upon each other's resources.

That all being said, I don't think your first story is unworkable, just needs a couple of modifications. Perhaps the Necron Lord offers humanity protection from the zombies (as well as immortality, to sweeten the deal), in exchange for wiping out the Eldar. Once the tomb has been allowed to awaken, the Lord keeps his bargain - but only a few of the ranking humans are given truly sentient forms. The vast majority are sealed up in Warrior chassis, swelling the Lord's legions.

Of course, personally, I prefer the second one. Sounds much more pirate-y.