Not choosing to spread the cure for the Krogan and then trying to lie to Wrex.
Nothing wicked about not wanting an ultra-violent race of man turtle brutes to multiply faster than rats without any kind of cultural reform. I personally killed Wrex back in ME1 for pointing his weapon at Shepard, so I didn't need to worry about lying to him.
And push that guy out of the window in Mass Effect 2.
Nothing wicked about killing a merc when the alternative is allow him to run free in the middle of a battle where i'm engaging his comrades.
U.S paratroops executed plenty of surrendered german troops on D-Day as they couldn't afford to be bogged down by taking care of them and the alternative of letting them go was stupid as hell, the same principle applies here.
How about letting hundreds of civilians burn alive so a merc can get revenge on a petty warlord?
Unlike those civilians, Zaeed's the one that'll have Shepard's back in the SM. So having him focused on his game is more important.
There were only a handful of civilians killed btw.