Based on what I've seen the cover mechanic it is viable in PVP. There are different specs of course the greatly impact how viable it is.

What cover does not protect you from though is Crowd Control. There are lot of CC moves that can knock out of cover.

First off, let me just explain how cover works. When your are hiding behind cover you don't take damage from direct attacks. You can still be hit from behind cover, but only when your using your own attacks. When you are properly covered you also get a damage bonus which doubles the damage your attacks cause. It is possible to be in cover and not get the damage upgrade though if you can only get partial cover. For instance if you're behind a box, but the enemy is located far enough to side to get line of sight on your back you don't get the damage upgrade.

As of right now, (meaning this is still subject to change until the game actually comes out), the Smuggler and the Agent both get a out of combat stealth in the same advanced class as their healing trees. So they each have an Advanced spec that is hybrid between a priest and a traditional Rouge/Thief. Those specs rely on Cover a lot less.

The Smuggler and Agent's other advanced classes are much more focused on using cover. They actually each have a skill tree that focuses on cover almost exclusively. Those trees also posses a skill that makes you immune to crowd control while your cover.

If you have a Cover Focused AC and your specced right it can very difficult to force you out of cover. Cover can eventually be destroyed if it takes enough damage though, but in general cover is pretty bulky.