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I was at a tournament this weekend and played against a Grey Hunter List that was using Sisters of Battle as allies. It wasn't a real serious tournament so I didn't really care but I wondered it was even legal?

You can take Witch Hunters as allied units in any Space Marine army variant, which would seem to include Grey Knights.

So yes, it's legal... so long as he has the appropriate rules.

He needs to have the Witchhunter codex with the page that states they can be taken as allies. If he doesn't have it, then no he cannot.