As with most of the polarized arguments here, I think the "why" falls somewhere in the middle of these two extremes.
As a700 states, they didn't move the world to keep him, so to some degree, they didn't want him. That's not the same as absolutely wanting to be rid of him, though. I don't think he'd be on his way out if there wasn't a better offer to leave to, which is to say, take away the opportunity with the Cubs, and I think he's still the GM. The FO didn't want him enough to increase his role with the team, in other words, they didn't evaluate his performance as good enough to continue the progression of his career with them. That does show some indication that they weren't totally pleased with his work. Ultimately, the Cubs offer provided a convenient means of separation. The FO could move on to the next thing....which really isn't bad timing for them, because if you are going to institute big changes, ie "clean house", it's best to get as many rooms as you can in one sweep....without the boat rocking caused by a firing.