If your DS is in a religious school, and he tolerates it for social reasons, I can see how it would be difficult for him to also tolerate a weekly ritual at home. It does appear that he's a nonbeliever immersed in a believer's world, and that could get a little suffocating... especially at a time when children are expected to begin aggressively asserting their individual identity.
I take it as a good sign that he still wants to enjoy the meal. I interpret that as meaning he is not rejecting family... just the ritual.
If the weekly ritual were all the religion he were exposed to, then in your place I might insist that he remain in place for the entire ritual meal, under the "We are a family, and we do this as a family" argument. However, given the extenuating circumstances of being in a religious school 35+ hours a week, I would give him a pass on the ritual portions of the meal, which seems convenient given your description of how it takes place. I would invite him to join the table after the beginning prayer is completed, and allow him to excuse himself before the ending prayer. I would also stipulate that he should do these things as unobtrusively as he can, and that commentary, verbal or otherwise, at the time is neither welcome nor appropriate. In this way, I think, you could both show tolerance to each other's views.
