Global damage change will grossly affect play balance. Long-ranged units become less useful in such cases, as close combat units can get in and do damage before being destroyed rather than simply being obliterated before touching their opponent. If you implement such a feature, expect lots of flamethrower and lightning action in low-damage mode, and lots of long-ranged action in high-damage mode.
Still, mutators would be nice. I think going through the LUA script system would be best - include an "onmod" event which lets the player iterate through the unit classes and weapon classes and allows them to make adjustments to attribute values of the classes.
