Sadly not a lot. Rogues are the single worst enemy a hunter has.
There is very very little you can do once a rogue is on top of you, and applies his poisons.
However there is a few things that **might** help you survive.
Activate your masters call if you see the rogue go into stealth and coming towards you.
If you see him coming to you, dot the bugger with a serpent sting. Keep them in combat.
Free action potion helps a LOT. So having a few of these potions always on you when you enter a BG can mean the difference between life and death when a rogue is gonna attack you. If you see a rogue coming to you and he enters stealth... drink that potion. 30 sec's will give you enough time to get close to another player that can help you should the bugger jump you.
As a marksman hunter the one thing that can help, is to macro your raptor strike + wingclip together and also you would need to double disengage... (Hence I said double disengage... Disengage --> readiness ---> disengage.)
Also keep a frost trap out around your feet if you suspect one is close by.
Always play with detect invisible units on in your tracking.
Very few survival hunters spec scatter shot... but to be honest if you face a decent rogue it wont help you... they will dismantle you leaving you with no weapon to even fire....
Sadly this is one area I will just run for my life or stick close by to other players that can help should they jump you.
The last option is to make sure you have full HP... Remember rogues are cowards ! They always gank the players with low HP... they would never dare attack someone with full HP

Or if you want them to run away in fear, just ensure you have your PVP trinket that removes all slowing / stunning effects. Rogues are renowned to run away like the cowards they are, the second you get to fight back.
Edit : Oh yes, next patch deterrence will work from behind now as well... So we no longer have to face the melee dps'er to make deterrence work.