While you can still fight effectively as a gunslinger without using cover, you're probably going to be doing about 20% less damage in a normal pve fight. What you need to do is to get into cover, blow off your charged burst, do quick shot, throw your charge, aim shot, do something else (any 1.5 sec ability), then quick shot again. Get out of cover, re-enter cover and do something similar.
As a Sharp Shooter, you get so many buffs from being behind cover, that it's not really worth it to not use it. You get damage reduction which helps healers, you get extra energy which is invaluable, you get the instant charged burst, you can't use aimed shot without it, and when you exit cover, you get increased damage reduction. Basically, for a sharp shooter, you will have to use cover. For saboteur, which is a ton of fun, but hard to use in pve due to it being aoe heavy, you don't have as much abilities that require being behind cover and you can usually dot up entire groups of enemies and burn them down. I haven't tried scrapper, but from what I understand, it's mostly about staying close to your mobs and using your physical attacks.
If you don't like the cover mechanic in other words, you'd probably be better off playing as a trooper. But barring that, a saboteur is a good replacement.