The problem is there is nothing they can do sans bring her on the ship, which will likely cause some hoodoo to happen.
The pruning phenomenon itself is basically an auto incinerator, so reality itself is a jackass.
Thing is, while it might be the right thing to do to say nothing and not intervene, that would change you into something probably less palatable than making the attempt, failing but still wanting to try.
Ehh, I can't really see it. Even if they shifted the tone, the theme still seems like, "show off the good side of this asshole, to make him the commander he could be", which is fine, but its turning into kissing his ass a little too quickly for that type of setup.
He should earn his stripes, then get the nakama hugs and shit, not "oh, what he really means is he likes you, don't mind the bumbling and overly harsh stupid crap". If you're trying to teach someone to grow, then becoming a sycophant isn't really doing it. Turns into making excuses for shitty behavior.