I think it all depends on how they are interpreted. Serenity Painted Death is a part of a storyline where one character wants revenge, correct? For this reason, the notion itself is still pretty sick but the fact that it is in a story seems to separate it a bit from being so 'evil'.
If songs like Bleak and The Leper Affinity are simply understood to be songs of rape and murder, then I would easily say that they are definitely evil and sick-minded in theme. The songs themselves seem a little vague, though, and if they are metaphorical or representative of something else, I wouldnt feel like they are quite so evil. Did Mikael ever state his intentions with these?
Same goes with Ghost of Perdition. Was it ever confirmed that it is about killing one's mother? If so I would consider it evil, but it too seems a little vague. When I read it, it doesnt seem so much like murder to me as just the mother figure being overtaken by dark supernatural powers, which could also be metaphorical and not simply disgusting rape/murder. (mother figures could easily be metaphorical, and the supernatural stuff could represent possession in general)
Do you really think Opeth writes evil lyrics to be blatantly "death metal evil", or do you think they make the more evil lyrics kinda vague so that they will be interpreted in more universal and less disgusting ways? They seem mature enough in their music and interviews that they wouldnt be so blatantly evil without reason...especially because Mikael claims to hate the evil in the world and I'm sure he would not intend to plant any seeds of it. Really I hope the lyrics are more sophisticated than simply being poetic depictions of rape and murder.