In rated bg,s I would assume the enemy is on their toes constantly, but in normal bg,s it is possible to stealth cap.
As I have played a rogue over the years I have observed how many people in Arathi Basin for example just afk while they are 'defending' the flag.
Ever tried to cap the flag when they are just standing there? I have done it so many times I am amazed by it.
Otherwise Sap works too and Blind. :P (rogues only)
But I advise you to try it, or rogue go with stealth, try to cap the flag, do nothing to the defenders, there is a chance they will not notice or are afk.
I just now even got a flag cap on my own at the blacksmith in AB, 2 dk,s were defending, sapped one, blinded the other, capped and vanished.