Yeah, the narration if you're off in Llewdor when Manannan comes back implies that Manannan was about to off you, but then he changes his mind and just sends you back home. So it is a brief moment of mercy. That said, I don't think you can use that as evidence that Manannan was actually not totally evil. After all, just because he wasn't as purely evil as possible doesn't mean that he wasn't evil.
So I'm also in the camp of seeing Manannan as very evil. It doesn't bother me that TSL is giving him a bit of internal conflict though. If anything, that kind of slight good side just makes Manannan all the more infuriatingly evil. He's not pure evil, he knows what he's doing is wrong, yet he does it anyway. He's too morally weak to take a stand and he just justifies it as following orders. He's like the Nazi officers put on trial at the end of the war who basically had the defense of "Well, what could I have done?" How about you do what's right? The good in Manannan doesn't complicate the character by making him more likable. It kind of does the opposite. It makes him more evil, just a different kind of evil than we thought.