Destiny is generally supposed to be faster than Halo, so your typical one headshot kill / multiple body shot kill seems about right for your standard power sniper, though more shots would be expected for something like a scout rifle or when facing an opponent with stronger armor.
Nothing breaks the continuity of the game like getting sniped. There you are fighting along, minding your own business, and then some joker tucked away in a remote safe house catches sight of you, spends a few seconds tracking you and then blam, it's over with no risk to him. That is lame lame lame lame. It's like bicycles driving on the road with cars. They just don't mix. Sniping is a completely separate game than combat soldiering. Let's face it, it's target practice. So I vote more than two shots anywhere, but allot points based on a hit, not on a kill. That way, he gets his jollies, and I don't get taken out from behind a bush 450 meters away.
1 kill with a headshot, 2 shots to the body. Keeping it skillful and award those who are good aimers but at the same time keeping it simple (2 shots to body)to avoid frustration.
Headshot kill for sure...if the player plays strategically, he will keep to cover and avoid open areas which snipers will keep a watch over. Additionally, with movement abilities like "blink" it should be pretty challenging to get a headshot.
A sniper is meant to be lethal and two shots to the head for a kill would be unrealistic...even for a magically enhanced being. "Shields" could play a role in diffusing this but we'll just have to see.
Personally I would say depends on how the aiming works, if its CoD style with locking then three shots anywhere if it takes actual aiming skill one shot to head two to body.