Playing around with the feature I bit I think that the "Toggle Breakpoint" command should appear visible in the menu at all times (as the other commands do) and simply enable/disable as R scripts are activated and deactivated. You could do this in the scheduleFinally block of onActivate here:

https://github.com/rstudio/rstudio/blob/master/src/gwt/src/org/rstudio/studio/client/workbench/views/source/editors/text/TextEditingTarget.java#L1235