Yes, it does seem that the RNC could disqualify Cruz, but that would not settle the issue of others in a situation like Cruz.
I believe the original intent of the ‘natural born citizen’ clause will carry the day when the original intent of the ‘general welfare’, ‘interstate commerce’, ‘Congress shall make no law’ and ‘shall not be infringed’ clauses are taken seriously.
We'll see. "Not naturalized" (which isn't exactly the same as NBC) doesn't lend itself to as much nuance as those other clauses, which are elastic as can be. The "naturalized" cases are numerous, and 100% in agreement on attaching "naturalized" to a person born abroad.
OTOH, the chances of a federal court deciding the issue are minuscule.