Personally, I liked how the Iron Kingdoms (d20/3.5) did their gun mages. They were either casting spells through the gun as an implement, which damaged the gun, or making their own magical rounds with spells imbued into the bullet, primarily ray and touch spells. They could create semi-magical guns that didn't take spell damage, like a rune-inscribed pistol or rifle. Lorewise, it was a new development, following the widespread production of firearms, so there was lots of resentment from entrenched magic users and great interest from national militaries looking to exploit the new thing. Lots of room to explore.