I found out if you take out legion soldiers from a far while hidden, and no other legions see the death, you can actually pick them off one by one without ever getting vilified even after killing Dead Sea using stealth boy. I have cleared Nipton, saved the Powder Gangers in Booted and it's surrounding camps, done Back in your own backyard using this method.

It is very useful for me as those assassins sent after me sometimes ends up killing civilians as well thus ending some quest or merchants.

My question is, how long I can keep doing this? I have not yet see Mr. House as I want to finish off as much side quest first as I can before doing the main quest or point of no return. At what point/quest I will get vilified?

never. if you sneak kill enemies with a melee weapon or suppressed firearm, you can do this forever.