I've never felt particularly bad for killing guards in the assassins creed series. It was really easy in #1 where the guards were constantly dragging people off for no reason, extorting money from random people. They were criminals in uniform.
In AC2 and it's (too many) sequels, if you accidentally bumped into a guard they would try and beat the crap out of you. If you dared climb a ladder to a rooftop, they would shout once and then start shooting at you, even if you're in a normal area of the city. I mean what, some shmuck goes to hand his laundry on the roof and "HEY! YOU ARE NOT-A ALLOWED UP-A HERE!" "But, I own this house, it's my roof... OH MY GOD YOU SHOT ME WITH AN ARROW! WHAT IS WRONG WITH YOU?!"
I did eventually start to wonder if the rooftop guards got hazard pay though, given that I went out of my way to kill every one of them I could... especially in brotherhood where having the crossbow just makes it way too easy to pick them off.
TL;DR Fuck the guards. Kill 'em, loot 'em, toss their bodies on to the street as a warning to others to consider less fatal occupations.