I think I understand what you are saying, however, I think that there is a difference between 'judgement' and 'sentencing." Judgement determines guilt, whereas sentencing determines punishment. It is a subtle difference, I admit.
I think you feel that he probably will have a lesser punishment by accepting a plea deal, because he is accepting less guilt this way than he potentially could have been judged for had it gone to jury (for instance, he might have plead to racketeering, animal torture, but the deal didn't include gambling), whereas had it gone to jury all three might have been given a guilty verdict, and thus his punishment would have been more severe, having been judged guilty on more counts.
I certainly understand this logic - one should receive the consequences of all their actions rather than some. That is a matter of justice. However, I think that in legalities, there is always a risk/reward type deal. I can't pretend to understand why the prosecution offered the deal they did - perhaps it will serve to bring more to justice, rather than only punishing the one. Perhaps there was a chance justice wouldn't be served to their satisfaction in their trial.