First off, it's assumed that a party of adventurers aren't a bunch of two-bit mickeymouse amateurs so terrible at going in and bringing war to the enemy that they fail to communicate. Even if the rogue is hidden away, his buddy is able to say 'There's a guy over here' in one way or another. Given that the Rogue is not likely to be absolutely retarded, he'll be able to deduce there's an enemy somewhere.
Not to mention, he's -specifically trained- in the art of moving out and shooting or stabbing something. How do we know this? He -has the power to move out and shoot or stab something.- Just like we know a Wizard with Scorching Burst has the ability to summon bursts of flame. It's on the damn character sheet.
So, the rogue uses his natural training, pops out from hiding, and then in the same action, starts the murder. It happens in movies all the time.... suddenly the hero comes out from his hiding place and starts shooting guys with supercool accuracy. Is it how it happens irl? Irrelevant, this is a heroic fantasy game, not a real life combat simulator, and it doesn't even -pretend- to be a simulation of real-world martial warfare. It -does- try to simulate the cool moves and action you see in fantasy action movies, and that's the yardstick that must be used.
So, the rogue pops out.... and he's got the drop on the guy, because the rogue is just that quick and sneaky. Someone using a move action and then an attack is just a bit too slow, but the rogue can do both, so he gets the drop. Well, needless to say, after that, the rogue's cover is blown... but the rogue can then use a move action to head right back to his cover, Stealthing again.
Yes, this is how it is intended to work.