...Regarding the Franklin...
...How do you think she survived where the Enterprise clearly will not? She appears small enough that just three of those shredder drones or whatever should Swiss-cheese her for good. If the swarming folks aim to capture slaves or whatever, perhaps they went easy on the Franklin, knowing they'd get no captives otherwise. So she even gets to keep working weapons!
Or did she land first and get boarded only after that? She's conveniently flat where Kirk's ship is endowed. And it seems she's level on the ground at the mystery planet, and perhaps even attempts a landing rather than a docking at the starbase.
Timo Saloniemi
Some are guessing the Franklin did something to piss off these aliens. Perhaps the Franklin landed to set off the chain of events. Then you have a mostly intact ship.