Is there an issue with creating multiple repository workspaces in a single eclipse workspace for RTC?

No; I currently have multiple RTC workspaces loaded into a local Eclipse workspace (aka RTC sandbox).

So long as your project names don't collide you shouldn't have any problems.

Hi Abe,
No, you can have multiple workspaces loaded.
The only thing to be careful about is project name collisions/conflicts.

It's certainly technically possible, but the downside is that if that is an interesting configuration, there is no record of that configuration on the server that you can share with others.  Because of that, I always have exactly one repository workspace loaded into a given Eclipse workspace, and adjust the content of that repository workspace to match whatever configuration I happen to want (repository workspaces are very cheap and easy to define, so you should feel free to create as many as you want).