Use autoreload to reload a single pistol, and just normal reload to reload both, you can always keep one loaded simply by firing them separately. Same way halo 2 did it, basically.
Yea, I was just thinking more like what Halo 3 did since its a better system. Left trigger fires left weapon, right trigger fires right weapon, left bumper reloads left weapon, right bumper reloads right weapon. It would still be nice to be able to specify which key reloads which individual weapon, since people like me, that have tilt-scroll wheels (they move left and right), a great use of that wheel would be be click it left to reload left, click it right to reload right.