IMO it's a balancing mechanism; The hellstaff is powerful, but chews through its ammo more recklessly. Not a bad scheme, really.
It's supposed to chew ammo recklessly, because hell ammo is abundant. Remember the sabreclaws and how numerous they are?
It is more similar to the Plasma Rifle. You'd have to make it a hitscan weapon (like, say, the Dragon Claw) for it to be close to the Chaingun; Basing a connection on "it fires two shots at a time" alone is, well, poor.
Aspect-wise yes, it's more similar to the Plasma Rifle. But by power, I'd say the dragonclaw is stronger than hellstaff. The hellstaff does 3 damage, as opposed to plasma which does 5 and it's more of a power weapon in Doom than a general-usage weapon as the hellstaff is in Heretic.
Also, the much more common ammo and usage for the hellstaff than the energy cells, the 4-tic duration instead of 3, the lack of a cooldown.
Also, on something as small as firing one shot or two for clicking once, the "because its different from the original" isn't a great argument.
See my other argument, then, which is about firing two missiles from a simple click. It has the benefit that I don't have to concentrate on pressing the mouse to deliver two-shot bursts. In fact, considering that those fireballs only do 13.5 damage on average, a single shot from a single tap wouldn't be very useful. Two of them would only cause 27 damage, which is neither excessive nor wasting (I rarely ever got below 100 ammo in Heretic, and I suspect those wacky Sabreclaws for it).
Finally, what was it about not modifying original weapons' behaviours?