I want to kill some important (named) NPCs that belong to certain factions. The problem is, I cannot find a way to get away with it.

No matter how high the sneak skill or how silently that person is killed, without you being noticed, all the surrounding faction members turn immediately hostile.

I can kill unnamed faction people silently without any repercussions, but cannot kill someone named "Colonel X" or anybody else who has a name without becoming hostile. I also incur a reputation penalty with the faction in question when I kill an important person. Why is it that nobody can see or hear me commit a murder, but everyone knows it is me regardless?

I guess this is a forum filled with pacifists...

You wait for them to go to sleep, then sneak up on them and plant a frag grenade in their inventory.

I used this to kill off the Great Khan leaders, and none of them attacked me

This has always bugged me, in just about every game that's had a 'faction' system

Experiment with wearing disguises before, during, and after the crime - especially the uniform of the victim's faction. I haven't tried it myself but from what I've read it will have a significant effect on reactions to crimes committed.

I have taken out a lot of named NPCs with no impact on faction with long range sniping one-shot headshots while [HIDDEN]. Just make sure you are far enough away that you will remain hidden after you shoot. You need a lot of points in guns, and you need a good sniper rifle. An alternative to this is using a stealth boy. In a lot of situations you can kill someone in a room filled with people and get away with it with no faction hit.