I very much doubt that they would ever seem themselves as bad guys even if they were fighting other humans such as chaos bands or even any groups that may want to break away from the Imperium
This is mainy because noone ever does see themselves as the bad guys as it comes to war do you think the German troops did during WW2? The Scots when fighting the English during the uprising depicted in braveheart? The Americans fighting the Vietcong? Each time there is a war each side fights for a different reason, neither side is good or evil theres just a reason pushing each side to war. At the end of the day most of the good or evil "fluff" after a war was written by the victors!