From the point of view of the writers, this move is quite understandable - the answer is simple. The point is to save the main villain for the sequel. But if you try to understand the character's action, then you will have to take into account his emotions, not logic. It probably hurt the Spider to lose a loved one, although he was aware that Quaritch was not his father, but a clone. Moreover, the colonel showed paternal feelings for him. After being rescued, the Spider, however, does not stay with Quaritch, which means he is still with the Na'vi at heart.