Fluff-wide, totally. Over half of the mechanicus turned traitor during the heresy. It's called the dark mechanicus.
Gamewise, certzinly anything goes. They're come the apocalypse so you need to respect the restrictions (not being able to deploy within 12" for example). The armies wouldn't be able to interact with each other (like casting psychic buffs and the sort
Alternatively, and this is what I do, you can ask your local group to cut you some slack and let you play them as battle brothers. There's not TOO much to be gained from it in my honest opinion, but it makes deployment a bit easier.
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