DPS is just that, damage per second. It really doesn't matter if it takes 5 seconds, if your DPS for missles is 50 and dps for lasers is 50, your giving up 250 points of damage by reloading either weapon type.
Reloading doesn't start until the cycle is complete, and they can fire immediately afterwards, so weapon cycle time isn't relevant. You just plain lose 5 seconds of dps.
What I was trying to say, is if giving up 250 damage (for instance) is too high a price to pay, then maybe the extension needs to be tweaked to give a faster reload, but it shouldn't matter which type of weapon your attempting to realod. And as OP was saying, if its bot based, maybe light bots could simply start with a faster reload if there is an imbalance in smalls and mediums.
The other obvious thing is that t4 weapons hold less ammo, and have to reload more often. Giving better reloads would need to be balance for that, that is better reload times would make T4 more powerful, and if that's not desirable from a balance perspective, the capacity of the T4 may have to be reduced to compensate for potentially faster reload.