I think a big part is the general obtuseness of the weapon : pistols, smgs, melee weapons, ect, are very ergonomic, small, light, and easy to point and fire, and these factors are abstracted into this : TU's is an approximation of what a person can do for an entire turn : running, opening doors, turning, grabbing things, moving equipment, ect, and pistols and SMGS handle better. Because of this, its not so much "a pistols fire rate" compared to "a rifles fire rate" but rather how easy it would be to fire a weapon, particularly in the middle of other tasks. Aiming a pistol and firing, while running around, opening doors, ect, is a LOT faster than aiming with a rifle while doing it, due to the fact you only need a 1 hand grip, its lighter, shorter, ect, thus, lower TU's
....Granted, it would be nice to get a separate stat to say, dictate the fire rate of different guns seperate from just "how much TU's", enabling factors such as having "true automatics" have a better ability to spit more rounds than a pistol per round, being able to move and fire without either one taking TU's away from other tasks.. (as well as making akimbo guns a pheasable technique) But this is a tall task, and kinda off topic.
TL;DR : TU cost isn't just about fire rate, its about how the gun handles too.