Renaming of Team Projects is one of the most requested feature on Visual Studio User Voice:
Figure 1: Team Project rename suggestion on User Voice
Today, Brian Harry announced new Visual Studio Online Update and it contains this feature, even if it will not be available to everyone at the beginning. For those people that uses TFS on-premise you will have this feature in the upcoming new version: TFS 2015.
I strongly suggests you to have a look at Visual Studio User Voice and give your suggestion, because it is in the radar of Visual Studio Team.