have you tried going into program files and finding the sins exe icon? if that works just creat a shortcut

Hmm that kind of sucks,  especially because this is a beta...  I don't know why Ironclad wouldn't have used a separate directory to install the expansion so that you could play either version of the game. 

If it isn't separated at launch, they should expect some mighty disgruntled customers.  Especially seeing as you aren't able to join regular sins games once you have the expansion installed (at least with the beta you can't at the moment).

You do realize that at release it's supposed to be that if you have entrenchment and you join a game that doesn't have entrenchment, it just plays the game without the entrenchment content. Don't worry it will work at release.