No, Jefferson was just one of the ornery people who blocked it. It's odd to try to rationalize support for the institution of slavery as striking a blow for emancipation.
Some progress is better than no progress. It was called a "compromise", after all. The Constitution contained both the justification for emancipation, and the legal framework to enact it. The seeds were there, it was only a matter of time. The South saw that inevitability and seceded to try and avoid it.
If you have a theory about how it could have happened otherwise, I'd be interested to hear it.
Seriously. Jefferson wasn't a delegate at the constitutional convention. He was in France.