Is there any way that you can shoot a Legionary and not have the Legion assassins invoked, in other words having your sorry butt being chased be the Legionary assassins?

pretty sure they appear when you fail "beware teh wrath of cesar" or whatever that quest is. I suppose you could stealth kill them for no reputation loss before you side with a different faction

Largely, no, so long as though you've completed Render Unto Caesar.

You MIGHT be able to sneak-kill them without getting vilified, but that involves a LOT of save-scumming, and only works when you can set up an ambush.

I did not, this round, even get "beware the wrath of Cesar" message they just started my butt.

I find that if I am vilified and then kill many more legionaries then I will only be a Merciful Thug.

I doubt it is meant to happen, but it does and who am I to question the brilliant minds at Bethesda and Obsidian?

It also happens if you kill Vulpes in Nipton, they appeared immediately when I left town.
I usually don't kill high-ranking Legion members, because I hate being forever harassed three times a day by these assassins.

Stealth kill seems to work for me, except I botched one(turned around right as I was about to knife him) and ended up killing three legion members in my current game. But this is before I've done the quest that leads to getting your rep cleared.

Anti materiel rifle headshots from distance or a nice super sledge is awesome to them, leave no Assassin alive btw.