Depends on how much cover you're talking about. If I were to rule, it would need to be either total cover or somewhere that's heavily obscured visually, and if the Orc sees the rogue moving into the cover, then yes, disadvantage on the roll.
The rules don't say a Stealth check to hide is made at disadvantage when you are seen before attempting it, so you should be able to with normal chance, unless the DM says otherwise. All you need is the necessary obscurement. In fact, most of the time you are noticed when trying to hide (even while invisible)