Ok, after further review I have come to a conclusion:
CPU owners that have CPU players should be exempt from any penalties. Think of it like leveling up in a video game against the computer, the higher in level you go, the harder it is to beat the computer.
Now on the other hand, human owners that have CPU players should most definitely be penalized. I should think the penalty should come in the form of league taxes or league adjustments, maybe CPU penalty. This should increase a certain percentage for each level/league of play. Meaning it would be more costly for a human owner to have CPU players on a team the higher in level it reaches. Penalize them for each CPU player they have on the team, for each day.
Don't think human owners should be rewarded for having androids on their team, this could eventually lead to a mutiny of all human players at the higher levels. No human players at higher levels would ultimately cap the retirement age of most who realize this, or worse, retirement for good.
Subtract 1% for each CPU player from the team chemistry of ANY teams with CPU players, Overall, Offense, and Defense. That should also eliminate any desire to hold onto CPU players and make it more likely that owners would actually look to recruit human players more vigorously.
This is echoed in this thread as well
http://goallineblitz.com/game/forum_thread.pl?thread_id=4801067&page=2#44316710