Are there any benefits for eliminating Exalt forces on Covert Extraction?
One of the Covert Operations missions is Covert Extraction. The third and final objective, once you get your operative to safety, is as follows:
Eliminate the remaining EXALT forces, or get to the EVAC zone.
Are there any benefits to killing the EXALT forces instead of just fleeing?
Depending on where your forces are, it can be easier and faster to just kill the rest of them. They also drop whatever weapon they're using, and the soldier who kills them will get XP from it.
Other than that, feel free to GTFO in the Skyranger, since your operative has all the intel that the local government will need to destroy the cell on their own.