I think the MACO example is a really great starting point though: have a few "away teams" that can beam down or beam over and take care of things. The exception being when circumstance requires a specific officer. In Enterprise during the Xindi conflict, MACOs handled certain off-ship actions. I think a similar situation in another franchise is Stargate SG-1/Atlantis, where the bridge crews never leave the ship and instead utilize teams (such as SG-1 or AR-1).

Starfleet claims they are not a military organization, but beams down with phasers (or phase rifles). Why not get a special team who is experienced militarily and instill first-contact procedures, diplomacy, and, if the need requires it, a science personnel who is trained to defend themselves.

With as many red/yellow shirts who have died, it makes sense to not endanger your senior officers who would have died without plot armor. For their credit, the MACOs were a step up from their plain security personnel.