Agree with everybody. It's so satisfying, just go for it. Boone will love you for it. It doesn't seem to affect gameplay except Legion goon squads will constantly show up to try and kill you, but that's OK. More Legion ears to collect!
I had assassins once... At lvl 4... I want more now I can easily kill them, they had good loot.
My character (main) sides with house, but keeps on good terms with the legion, get to "liked" and get a safehouse, then you can get free supplies from the guy in the safehouse. 2 stealthboys every few days.
Its great for RPing too, its sweet irony that they are beaten at their own game of infiltraiting their foes and screwing [censored] up from the inside..