I've found that my luck against Rogues has been changing for the better in battlegrounds over the last few nights. I killed one Rogue in particular probably five times in a single Warsong Gulch match. There was also a Marks Hunter in the battleground who messaged me about having difficulty with them; once I told him about my method, he messaged me back and said he'd actually managed to kill one.
From what I've been able to learn, the main things Rogues have (at least that they use against me) are Cheap Shot, Kidney Shot, Crippling Poison, and their vanishing tricks.
You will still need probably at least 9k hitpoints to be able to do this, but the initial thing I do is tank the stuns until I see the text come up for Kidney Shot, and trinket then and only then. Once I've trinketed, I then drop Snake Trap, immediately feign, jump forward, apply Serpent Sting and Concussive Shot, and begin kiting. I'd also drink a health potion after you're able to start kiting as well, to make it more certain. A determined Rogue will probably still get a few hits in after you've dropped Snake Trap, even though what they primarily have to focus on then is getting away from the snakes.
The above doesn't work all the time. It won't work when my trinket is on cooldown, of course, and it also won't work against a good Subtlety Rogue who knows to use Shadowstep and their other means of re-entering stealth, mainly because I can't keep them targetted. It would also likely only work in the Arena if I was in a scenario where I wasn't being hit by more than one person at a time, and that virtually never happens.
For people who wonder how I can try to hand out PvP advice when my Arena ratings are so bad, I can only say that it's because truthfully, the Arena is extremely difficult; I have a lot of trouble there. People also seem to kill me as a Hunter before my other teammates, more or less consistently. It isn't impossible; I've been in a couple of good winning matches...but it is very hard.