For some reason, the "ok, let's just RUN and go live in hiding" temptation of the main character scene is always incredibly divisive in any work that has it: it's either really good, or really bad, and it seems to create anger simply by existing. Remember the shitstorm around a similar scene in Re:Zero?
Skellington has a secret sidequest to complete, a long term goal he's working toward, and has repeatedly told Rena that he really doesn't care any more for her than for any of the other people he's tried to protect. He's using her to further his own agenda, the same way she used him back in the 'lure targets into the dungeon' plot, and while she may have developed feeling for him, he's never seemed to reciprocate beyond a business relationship and fulfilling his promises to protect her.
If she ends up backstabbing him, it's going to be because it's obvious that he's just using her (which she makes pretty obvious by telling him that he's the one who wants her promoted, despite her wishes). Hell hath no fury, and all that.
@truepurple The MC has a rather male-looking skeleton, with the pronounced brow and jaw, narrower male-style pelvis, and broader shoulders that result from the male growth pattern. I'm not sure it matters (because it's fairly clear he's probably asexual), but 'ze'/'zir' is really hard to read.