Not that this makes Whedon less of a jerk, but I do think he had some legitimate complaints about Carpenter.
Oh, come on. Any time we have a sentence of the form, "Not that this means X, but...," the effect is to press X.
Folks on the set could not leave Whedon alone with an underage female cast member, for fear of the abuse he'd put upon her. Whatever "legitimate complaints" he had are irrelevant in comparison to that.