By all means, killing hunters is a noble pursuit. However, you should never fight a hunter 1v1. If unavoidable, such as in a duel, a fine strategy is to wait until the hunter gets bored and either forfeits, giving you victory, or takes off his camo. Flying above the hunter so that he attacks you in the air and takes fall damage on the way down is also a valid strategy.
In group pvp targeting hunters should be the priority of a rogue, since their treachery will wreck havoc upon your team and, most importantly, you. When attacking an enemy (hunter or otherwise) who is targeting an allied hunter, it is polite to allow them to kill the hunter, before slaying your target.
Grouping with them:
Of course the safest bet is to avoid this situation, however there are a few ways of dealing with them.
First, in a raid situation, make friends with the raid leader. If that is you, don't do anything creepy, and why the heck did you invite a hunter!? Anyway if you can convince a leader that a drop is a bigger upgrade for you than for the hunter, or that the hunter clubs baby seals with kittens, then your chances for loot will go up.
"When life gives you lemons, make lemonade" - Old Proverb
In this case, the lemons are the hunters, and the lemonade is dead hunters. Blizzard gave us tricks of the trade for a reason, and I'll be damned if it isn't to ninja pull lots of mobs on hunters. Feign Death is on a longer CD than Tricks, and if the hunter decides to pull on you, well then you have a valid reason to kick em!
Much like hoes, you should never trust a hunter. I once saw Ghostcrawler, the tameable rare spawn. I attempted to kill it, but it soon became evident that the task was impossible, so I made the mistake of figuring I would give it to a hunter guildie, in return for his doing my bidding. This was in the beginning of Cata, and he has yet to be of any use. In fact, the hunter did what they usually do: ran. In this case, he refused to log on for any reasonable amount of time when he found out he would need to help the great rogue who gave him a rare pet. Learn from my mistake, and make sure any hunters you do things for give you a large amount of compensation up-front.
That's all for now, I hope this PSA has enlightened you as to how to counter the hunter menace that has plagued the rogues of Azeroth for so long. And remember, the only good hunter is a dead hunter. And even then you really outta make sure he really is.