Sure, I get the moral directive that Kirk lays on M5. However, I don't think that much time elapsed between Wesley's report and their retreating outside of phaser range - which is a considerable distance.
The only options for the crew of the Excalibur are
1) escape by shuttles
2) escape by primary hull detachment
3) escape by beam out to friendly ships
1 and 2 didn't occur so that leaves 3. It is possible during that time when M5 turned to chase Potemkin that Lexington and Hood moved in and beamed out the survivors. If that is the case, then this is an interesting example of the ability to beam a whole bunch of people by a starship(s).
However, I'd imagine the dead bodies stayed aboard for Kirk's strategy to work.
You misunderstood what I was saying. You must be thinking of a different scene.
The fragmentation of time I was talking about took place here:
WESLEY: The Enterprise looks dead! I'm going to take a chance he's not just laying a trap. Wesley to attack force.
WESLEY [OC]: Break off attack! Do not fire! The Enterprise has dropped her shields. I repeat, hold attack! Do not fire!
[Enterprise flying in space] <<<<<--- HERE!!!
MCCOY: He'll have to be committed to a total rehabilitation center. Right now he's under sedation, heavy restraints.
SPOCK: I would say his multitronic unit is in approximately the same condition.
KIRK: That's exactly the situation I was hoping for when I forced the M-5 to realize it had committed murder.
(The group walk out of the medical bay to McCoy's office.)
KIRK: Daystrom felt such an act was against the laws of God and man. The computer that carried his engrams also believed it.
The Enterprise establishment shot can be used to indicate the fragmentation of time. It's an old trick that was used throughout the series. We have no idea how long after Wesley's cease-fire order (the ending of the war-games) that Kirk, Spock and McCoy were in Sickbay talking over Daystrom's sleeping body. It could've been 2 hours, 2 days or 2 weeks. But the Enterprise's flying-in-space shot is a sure cue without any spoken words necessary: it says simply "later..."
My theory is that M-5, using Enterprise's scanners at a distance, could not detect survivors aboard the damaged and derelict Excalibur. ("For the World Is Hollow And I Have Touched the Sky", "TNG's "Heart of Glory") So everyone, including the M-5, assumed that without any indication of life signs, all the Excalibur crew had perished.
But after Wesley's cease-fire
, it's entirely possible (and makes sense, given the improved humor and a joking Kirk and company) that survivors had been found and rescued from the drifting Excalibur. It would also make sense if some of those survivors were brought aboard the Enterprise to recover the ship's systems so she could return to the space station. (Remember, there's no longer an M-5 to run the ship, only 19 visibly relieved and relaxed Enterprise staff aboard. Excalibur survivors could be helping Scotty in the Engine Room, manning the engines, pulling out M-5's plugs, etc.)