Well even if that stuff happened in GZ they could still split the timeline.
Would be better then just doing another "missng chapter in the Big Boss saga" that they have been doing since MGS3 that is a random story that has nothing to do with anything exept for the very end when someone says "outer heaven"
I think it's too hard to say at this point if this is Ground Zeroes or another game, especially since MGS 5 has already been announced and talked about by Kojima in the past. It's all really up in the air I think at this point.
IIRC, they were literally going to call the game "MGS III" and then people would be all, "What the fuck, what happened to 2!?" and they would play through the Plant sequence with Raiden, then after finishing the main game, you'd unlock "MGS II" with Snake on the Tanker explaining all that went down there.