Still can't say I'm inspired to play an Agent just yet...
I started an Agent and a Smuggler at the same time. Played them both up for a little while, to compare.
First off, the Agent uses a pistol during cinematics, but can't really use one at all.
More importantly, the Agent gets hit more often while charging abilities. Charged Shot leaves the Smuggler behind cover while charging, then they stand up long enough to fire. Sniper Shot leaves the Agent standing while charging, so they get hit more (and suffer knockback) before eventually firing.
It's the little things, that made me delete the Agent eventually and play up the Smuggler instead.
Your claim of being "knocked back" I assume you mean pushback. I hate to tell you that regardless of the standing or behind cover does not affect pushback. Snipers/gunslingers cannot have abilities pushed back. As long as you are in cover you are immune to pushback and interrupts, regardless if your character's animation is standing or hiding.