I have a solution in Visual Studio 2008 which has multiple projects. One of the projects is a WCF project. Sometimes I just want to debug other projects, but when I press F5
You could try to unload the WCF project in the solution, then debug.
Sorry it was late I misread the last part to fast, then the only other way, that I know of, is to comment out the web parts in the Property Group of the project. This prevented the pop-up for me
Unload the project, Comment out the mentioned part, reload.