I favor the idea that everyone is trying to do the right thing as best as they are able. However, that doesn't mean they'll succeed or even that their methods make any sense in the first place. Conflict between characters like the moon wars and the religion wars doesn't mean that one side or the other is wrong, just that they have different perspectives. I can sympathize with both Yukari and the Watatsukis, with Byakuren and Miko. None of them are bad people, they just have different values and beliefs that put them in conflict.
Except Tenshi. I hate Tenshi. :V
Also, I'm not sure they're really out of place. The discussion between Byakuren and Miko in SoPM basically mirrors the discussion between Kasen and Reimu in WaHH, which itself goes back to ideas brought up by Keine in BAiJR. The human-youkai conflict and whether peace is possible or desirable is one of the central themes of the series.