I'm not sure what kind of flash setup you're using, but if raising ISO or lowering aperture is increasing exposure from eTTL flash then you are most likely bumping up against the max flash power. In those situations your choices are:
- Move flash closer to subject
- Increase number of flashes
- Increase ISO
- Open Aperture
As a point of disussion, eTTL should work just fine in low light conditions with stage lighting, within reason anyway. Are you using on-camera or off-camera flash? How far away are you (in a pit or audience)? What kind of exposure settings are we talking about without flash? If the stage lighting is too dim then you can't expect to use flash without completely changing the lighting, but usually stage lighting is rather bright, so everyone in the audience can see.
