I save your president, enlist the Boomers, vanquish the Great Khans, foil the Omertas plan, and destroy the Brotherhood of Steel. Yet I'm a " Dark Hero"? WTF. Why does killing a squatter destroy my rep? I don't understand it. I do the freaking Talent Pool quest and become idolized on the strip. I shot Mortimer in the god damned face. Still idolized.
Sorry. You can pile all the good deeds in the world on one side and they won''t counterbalance murder.
As for Mortimer, you can kill him in self defense. Failing that you will lose rep with his faction for killing him. This is common throughout the game. In fact, sometimes you can commit an act that costs you rep with one faction and gains you fame with another.