I'm having the same issue, and while this is not a fix, it is another work around.
If you have more than one web project in the solution, set one of the other ones as the startup project. After Update 2, when debugging, IIS Express is starting all (I tried a solution with 2, so at least in that case it was both) regardless of which one is the startup project. VS will only launch the startup project, but if you look at the Applications list in IIS Express it will show all of them. If you stop debugging, the startup project will stop, but the other(s) will still be running.
So in my case, with two web projects, I set the other one as the startup project, and I'm able to continue working as I had before the update.