While the SOL for grand theft certainly has not expired, the business entered into a contractual arrangement with the "suspect." Most DAs would not touch this at this point because it is now, arguably, a civil matter.
But! The agreement is with YOU, not with your son - the suspect. If the agreement is worded properly, it may not prevent the DA from filing at all. And while prosecutors are reluctant to file in situations that have become civil in nature, there is nothing to prevent them from doing so.
The question now becomes one of whether or not you and your son want to call the business's bluff.
And why are you going to put yourself on the line to keep your son out of jail? HE stole from the business, not you. HE needs to pay the piper, not you. If charges ARE filed, and he IS prosecuted, it is because your SON committed a serious crime. HIS actions led to this.
And before anyone asks whether or not I would allow my son to go to jail under a similar circumstances, the answer is, "Yes." I would not have paid back a penny on his behalf. By keeping him from feeling the consequences of his actions he will have learned nothing. All he will know is that his parents will protect him from the consequences of poor and even illegal decisions, and he will continue to do the same. You have set a precedent that he will almost certainly use to make you feel guilty the next time he gets in trouble, too. I have seen this a hundred times, and the kids (yes, even the 30 year old kids) are real sorry ... really sorry ... today. Tomorrow, there will be a new excuse, and another plea for aid ... and on it will go.
Does he have a drug problem? A gambling problem? Some other addiction or weakness that has encouraged this theft?