I was thinking of situations like in the TNG episode First Contact. The Federation is obviously aware of the aliens in that episode as there is a Starfleet team in deep cover on the planet monitoring them until such time as their culture is ready to make contact, which Picard and Deanna do in this episode. Even taking into account their making contact was more of an emergency situation brought on by them losing contact with Riker, you'd think there'd be someone from the Federation's diplomatic service involved with the matter who would be if not on board the Enterprise, at least based close enough near by that they could arrive relatively quickly in order to handle the first contact protocols.Absolutely. If it's the case of a starship happening upon a new civilization, then it makes sense that starship would make first contact. But if a new civilization has been found and a starship is specifically dispatched to make first contact, they should be able to bring a diplomat on.
Hell, the episode says the whole reason teams are sent in undercover is to prevent disastrous first contacts that result when there was too much ignorance about the race they were making contact with. Yet the matter of making contact is still an exclusively Starfleet matter rather than having any kind of government oversight with an actual diplomat present.
It is a rather troubling sign of how much trouble the Federation must be in if so many Starfleet Admirals turn out to be renegades and/or outright evil. Utopia seems to breed corruption.It bears repeating that Starfleet officers, including top admirals, members of Starfleet Command, tried to assassinate their own president. Yet, from what we can tell, it had absolutely no effect on the enormous trust the Federation places in Starfleet.