Wow, this was poorly thought out by the family of the bride, and/or by the bride and groom themselves! "It would not have been appropriate"??? Were you even asked for a list of guests so they could include your numbers in the ordering of enough invitations? Or was your side ("your sides") an afterthought?
So, if I understand this correctly, you are the mother of the groom, John Smith, but you married Mr. Jones and your son has been known as John Jones for his whole life? And no one on your side of the family knows that he is John Smith legally? For all these years? How close are they, then, that you would invite them to the wedding? And not only that, now you are trying to invite all of the Smiths too, since you get along great with your son's father? So a whole bunch of Smiths will come who don't know that your son is known as John Jones?
I may not have this figured out right, so excuse me if my suggestions are off.
I think an insert is a terrible idea - it tells all of the Joneses and the Smiths that they are an afterthought, that there was never any intention of making it clear to them who is getting married. I would write up (and pay for) however many invitations you need for your side/sides of the family, and perhaps use the same design/font/blah blah as the original. They won't know that another invitation went to the bride's family and the friends of the bride & groom. You can either have the reply envelope addressed to you (if everyone will know who you are) or to your ex (if everyone will know who he is) or go for 2 sets of reply envelopes, with the understanding that you have to collect all of these and get the info to the bride's family. It's cumbersome, but I can't imagine finding another way to tell people who the groom is.
You should also realize that a good percentage of the wedding guests will be hearing your son called by a different name than what they have assumed it to be for all these years, so there will be confusion on that day as well as with any gift registry info. (I personally hate that gift registry info goes in the invitations, but I realize many people do it - so if your friends and your ex's friends go to Macy's or Crate & Barrel to buy a gift, they will be completely confused by submitted the "wrong" name.)
I think it would be wise for the bride and groom to start looking at some etiquette books and wedding guides for blended families to start to figure out a whole host of things, from invitations (definitely a bit late!) to "first dance" to "who sits where and who gets escorted into the ceremony" and who makes the toasts and who pays and.....you get the idea.
I realize you are trying not to ruffle feathers with the bride's family, but I think the horse is already out of the barn on that one.
If I'm missing something in your post, I apologize and hope you will clarify in the bottom of the question with "ETA" or in the "SWH" section.