I would consult with another attorney regarding your son's case. Our office specializes in the defense of sex crimes. If you have any questions, I am available tomorrow after 830. My number is 4042176978.
A judge does not have to accept the negotiations between the State and the defense. The judge has the authority to reject the plea negotiations and sentence harsher than what was agreed to. Moreover, in sex cases, the judge can require the defendant to pay for the victim's future counseling. This proces will require the victim to submit bills to the court for the future counseling in order for your son to have to actually pay it. Also, the judge's sentence will cap the payments to the maximum amount ordered in the sentence.
At this point, your son could have withdrawn his plea and gone to trial. I assume he did not; he accepted the judge's alterations to the plea agreement. In such an instance, it will be very difficult to withdraw his plea. He would either have to show that his plea was involuntary or based upon incorrect advice (ineffective assistance) from his attorney. This is nearly impossible to show since most pleas are taken nowadays with written plea forms and questioning by the judge that address the voluntariness factors. Your son has already said multiple times that his plea was free and voluntary. Moreover, the lawyer is not likely to be found guilty to negotiating a plea to lesser included offenses that got your son out of the mandatory minimum sentences for rape, etc. The only possible avenue for withdrawing this plea is if the attorney advised your son about some point of law that was not correct.
In that instance, you have to consider whether attacking the plea is the right course of action. You may not like the additional probation and the counseling fees, but it is probably a better result still than what he will get if he goes to trial. Upon conviction for rape, he is no longer able to negotiate for a lower prison sentence. The mandatory minimum is 25 years in prison. Moreover, he could get more than 25 years. The judge has authority to sentence him to 35, 45, 55 years in prison. The judge actually can sentence him to life in prison. Therefore, the risk is enormous if your son successfully withdraws his plea.