Love the fact that factions reputations wont change if you sneak kill and no one see's you kill someone.

how many have you done? I was doing stealth kills and after 4 or 5, the infamy box popped up, never was discovered.

You need to make sure no one hears or sees the person die, so if they're out in the middle of nowhere you wont lose rep. You can also stealth kill someone with a supressed weapon. I've killed somewhere around 30-40 people with a supressed sniper and my rep is intact.