I launched 2 instances of SSMS just now and Source Control is disabled in second instance.
That's an acceptable limitation for a v1.0 product IMO, but what I found annoying is this. I closed the original instance so that the second instance with SSC disabled was now the only instance. I couldn't find any way to get it to enable itself in the second instance, which was now the only instance. I ended up closing this instance as well and launching SSMS a third time.
Its not a huge problem by any means, but definitely what I would consider an annoyance and usability issue as its not clearly indicated that you won't be able to use SSC in that instance. The dialog is worded in such a way that made me think SSC would become available after closing the other instance, which it didn't.
For the future, I would like to be able to use multiple instances of SSC, though. I often run multiple instances of SSMS connected to different databases on different monitors. Not having SSC in those other instances will definitely be annoying.