If he's anything near what he was AFTER returning from the injury Monday night, no question I'd sit him. While medically "cleared", he was a complete shell of himself and not able to function physically and mentally. Also recall the SF game Week 1, I believe he was so much mentally consumed with how to deal with his physical limitations and perhaps pain, his ability to perform suffered significantly.
Romo's tough, we know and respect that. He will gut it out if it's up to him. Sometimes it's best for someone to step in and make the decision for him.
So to answer the question, I would have to know how limited he is due to pain and stiffness. No one outside of Valley Ranch will really know that until 100 Sunday.