Its not even just a conscience. Homie had a panic attack at the sight of blood and combat, something he was likely seeing for the first time. Something strong enough to make him betray and abandon everything he knew and was raised with to escape.

And the rest of the movies just forget that and he is totes okay with violence and killing, as long as its the faceless bad guys (that he totally wasn't one of and should know are humans too) and his only reservations is being weaker than everyone else.