I wonder if Regina is telling the truth, that she let Kurt go, and whilst he was looking for Greg, the organisation came and kidnapped him.
In Skyfall, M said to Bond that “Orphans make the best recruits”. The same theory could apply to Greg and Tamara. What if Tamara’s “grandmother” was actually her handler?
I think there’s a high chance she really was telling the truth. If she still had Kurt locked up, wouldn’t she be willing to free him as a way to try to get Greg out of Storybrooke? It’s not out of the realm of possibility that Regina felt bad for Greg/Owen and let Kurt go shortly after he left, but something else happened.