I'll be honest, that thought had crossed my mind too Gibraltar!
However, the only OMEGA incident that canon offers us is on VOYAGER in the Delta Quadrant where the Omega Directive is initiated. (Voy : OMEGA DIRECTIVE)
According to MEMORY ALPHA (which references that episode):
The captain, absolutely forbidden from discussing anything about what was happening with any member of his/her crew, would contact Starfleet Command and inform them of the situation. Starfleet Command would then dispatch in a specialized team authorized to use whatever means necessary to destroy the molecules.
My interpretation was that the team would arrive and, discovering that the particle was not naturally occurring, reassess the situation to take into account Chariscarpia's unique situation.
Obviously events overrode that option, but I agree that destroying a controlled molecule doesn't make sense for two reasons.
1. This is a first contact with an advanced civilization that has obviously controlled the molecule, indicating to me at least that discussion is more important than action.
2. With the chance of exchanging information with Chariscarpia, the Federation would benefit greatly from obtaining that technology.
I suspect that Starfleet needs to inspect its modus operandi!