Clearly.
Not seeing that paying Quade $1M not to manage is a good thing, (as evidenced by his handling of the team in September) is beyond belief . Pena (for one) should have been benched for the callups to have playing time, but Pena was near ever present (89PA, in 22G in Sept). That alone should have been enough to seal his fate, he can only have been managing for his own record, not for the good of the team in the long run, when the season was clearly over for the cubs.