I think that "presumably" was either a foreshadowing or a commentary on the events of Might and Magic 8 (depending on when it was written). Let's not forget that it was the Ancients who set Escaton loose upon Enroth. Not a benevolent course of action.
Well I wouldnt say that creating weapon like Estacon would suggest that ancients are bad to some degree. Unless they have extremely naive personalities( which is only present for some comic superheroes like superman), creating such weapon is normal method of waging war. First of all , weapon is unleashed only at point when ancients believed that planet is doomed anyway due to infestation,(considering threat, there is no way they could individually try to save each and every planet) second of all, ancient programed him with sort of compassion which ultimately caused him to override his main protocols, even if not directly. If they would be sociopathic race , which wouldn't care, their AI's (ones that aren't totally went crazy like some particular Terra guardian) wouldn't be with built in compassion towards people, after all creators create personalities after themselves. If they would think compassion is not essential and human life is expendable, Estacon wouldn't try to save anything, nor Corak would be so nice to natives. Those qualities would be removed as flaws in first place.