The only dishonorable quests are probably the last Umpani and T'Rang ones (destroy the other's Mothership), and turning in Kunar (He is working for the T'Rang, which is a moot point because of the alliance).

Astral Dominae: 2 choices. Either pay Don Barlone, or whack him. I choose the latter, as doing it honorably still results in Rattkin harassment squads.

Chaos Moliri: There is no reason to whack the peaceful Mook, switch the fake Astral Dominae for the Chaos Moliri.

Destinae Dominus: Grab the artifact that he gives you (make sure to put it into the personal inventory of the character with the Helm of Serenity). There is no reason to kill him.