People from both companies work on the game...it is probably true that SD is more responsible for PR/marketing/sales and support while Ironclad focuses more on engine issues, but both are active in developing the game as well as it's expansions...
In fact, Fraiser was quite active on the forums during the release of Rebellion, specifically trying to nail some MD issues and engine related bugs...and of course, we have SD devs involved as well (Yarlen and Kryo are probably the two biggest for Sins)...
SD is busy with a lot of other things, but SD also has a lot more resources and personell than Ironclad...who picks up the ball on Sins 2 is unknown, but I wouldn't be surprised if both companies worked together again...point is, there are enough people between the two companies that current WIPs (like Sins of a Dark Age) shouldn't preclude the development of Sins 2...