Yes, not all Dragon Knights are good but they were made for a good purpose whereas the Dragon Slayers were not. The Dragon Slayers can be good people but what they are doing is an evil deed. BTW OP, you do get to speak to the dragon slayers you kill later on, as you meet them again, but since you have expressed that you're not playing the game any further because you have to kill people you've only known for two minutes, then there's no point in further discussion is there?
Having to kill Zandalor or The Divine would be more troubling and thankfully, nothing comes to that. Having to kill some random guys called Tom, Dick and Harry who you've only known for literally 2 minutes in the game is not troubling. The game claims I've known them for longer but you only literally speak with them for several seconds in the game and their role is rather minor which should make killing them (because they want to kill you) all the more easier.