It is always possible to get a pardon for a conviction, but the chances are very, very slim that one will be granted. There have been several high profile cases in the news lately about otherwise consensual sexual relationships turning into felony convictions for unaware males and females. In Texas, it is an affirmative defense (and I'm not sure that this defense was available 12 years ago when your son's case was active) to sexual assault of a child (what we call statutory rape in Texas) if the defendant is less than 3 years older than the victim. However, that defense only applies to children 14 and older.
Still, it may be possible to convince the Board of Pardons and Parole that your son's situation merits a pardon. Check out their website and perhaps consider calling a local attorney who handles pardons. Be warned, this can be an expensive process with a small chance of success. Good luck.
I agree with the other posting on this matter. I will add that pardons generally are endorsed when the defendant has done something extraordinary that should be given recognition. An example of this might be a defendant that acknowledged their crime, overcame certain obstacles, and then did some kind of social function that paid society back for that harm.
There is also the Presidential Pardon that is available. Both situations will require a very strong presentation of the facts, and the circumstances that occured back in the day and what is happening now. I would be happy to discuss this more with you.
This will be an expensive type of action and there is a strong chance of denial.