Hi Roland,
In order to disable breakpoints in KDS you need to go to the Breakpoints view on the Debug perspective:

Once there, you can disable the breakpoints by deselecting them:

Or you can delete the selected breakpoints by clicking on the X icon:

Another way too access the Breakpoints view is by clicking on Window>>Show View>>Breakpoints.
PS. Here is a post related to this topic that might also be helpful for you:
http://mcuoneclipse.com/2014/10/11/failed-to-debug-with-gdb-breakpoints-or-expressions-on-non-existi...
Best Regards!
Carlos