If you want to link a vita to an origin account, you actually have to link his whole PSN account to it.
In theory this should be done automatically, as long as you used the same email address for both accounts.
If the email addresses are different, this link might help you
http://help.ea.com/en/article/linking-your-gamertag-psn-id-or-ea-classic-screen-name/
As you can only link one PSN-account to an origin account and vice versa, I would suggest to create a new origin account and link it to his PSN persona to prevent future trouble and confusion.
The "not letting you create an acct" part confuses me a little. What exactly is preventing this? are you not asked to use origin at all ingame? If you could provide more details on this, it'd be easier to help.
Also just for completion: your son does have a PSN account, that he uses on the vita, right? if he doesn't this would be the first thing to do in order to play online at all...
