If I remember correctly, the Monitor was always planned to be a good guy in Crisis on Infinite Earths, but the intent was to fake out the reader since he'd spent the previous year supplying weaponry to the bad guys, his true purpose being to "test" the heroes and figure out who was suitable for saving the multiverse blah blah blah.
However, it seems that aside from the "use this guy in your stories" direction, the idea that the Monitor was supposed to be doing this for a "good" reason didn't filter down, so some writers played him as a straight villain instead of just enigmatic and ambiguous.