Devil's Advocate here:
Is it entirely possible that a defense in this scenario has 12 on the field, and one of those 12 don't realize they are a replaced player because the substitute didn't adequately inform his teammate?
The question is obviously rhetorical because it happens numerous times in just about every game, especially at a sub-varsity level. And I fully realize the "otherwise becomes a player"-verbiage.
To the original question, philosophically it's better to kill it and throw a 5-yarder for Illegal Substitution in order to avoid the potential 15-yard Illegal Participation. It's worth noting, however, that just because B has 12 on the field and the ball is snapped doesn't mean it's automatically Illegal Participation. A Live-Ball Illegal Substitution is still possible provided one of those 12 is not participating.