How can I make a villager have an... "accident"?
Lava
Carefully place a bucket of lava by your victim innocent bystander. Once they are aflame, pick it up again so it doesn't spread too far!
Fire
Light them on fire with flint & steel. You can punch out the flames immediately to minimize collateral damage.
Suffocation
Carefully dig a hole directly beneath them, and fill it in with sand/gravel.
Drowning
Construct a water flow that drowns them (look up some mob traps). 'Accidentally' knock them into it.
Zombie Apocalypse
Got access to a zombie spawner? 'Pipe' your zombies with water flows into the center of the village. Unless they've got an iron golem, there may be a few casualties.
Remember: It's not you, it's the hostile environment.
I just tested these two options in my village right next to an Iron Golem, and he didn't bat an eye...
Use a flint and steel to light the spot on the ground below them on fire, being careful not to hit them by accident. Then just let 'em burn. Oh, and be careful not to set anything else on fire when you do it. If anything else nearby catches, just punch it to extinguish it.
You can gently nudge villagers where you want them to go, so you could dig a 2-block deep hole next to the "mark", nudge them into the hole, then quickly drop a couple of sand or gravel blocks down on them from above to suffocate them.
You may need to exercise even more caution now with the pretty scary update, or your villagers won't reproduce after other villagers have "accidents." From the version history:
After a villager dies to natural causes, excluding mobs, while a player is within 16 blocks or if a mob kills a villager, no baby villagers will be produced in the next few minutes ( http://www.minecraftwiki.net/wiki/Version_history#1.4.2 )
You may want to send less useful villagers to serve out the rest of their lives in iron golem farms, or you could create some "death rails" for sending villagers who have outlived their usefulness 20 blocks away from the village to "a place where accidents happen"
Keep in mind that with the update and village reputation you'll want now more than ever to avoid direct involvement. Gary's mantra rings true:
Remember: It's not you, it's the hostile environment.