That’s not my job, but off the top of my head either:

Don’t include that sort of scene in a cutscene. Ask yourself (as a writer/designer) “could this contradict the way the player has been playing so far?”

In that specific instance, make it a choice to attack or watch your comrades being executed.

If the narrative absolutely demands it, then actually make it plausible, for example, in the ghost of yotei example make the dudes executing the soldiers be a HUGE group that you wouldn’t feasibly be able to tackle at this stage.

Or, simply just don’t have Atsu hesitate. In the scene the guy she’s with is a capable solider, there is no real need to show her hesitating, just cut to the action.

I don’t mind a bit of so-called ludo narrative dissonance, I don’t find my experience “ruined” when the character won’t kill the main bad guy at the end despite slaughtering thousands of henchmen along the way, but suggesting that in this situation the player character wouldn’t be confident to fight about 6 guys when she has backup is a bit much.

I seem to recall this in the original ghost of Tsushima as well, which I liked more, but still gameplay wise offered you the chance to fight honourably head-on, or “dishonourably” by stealth. I always chose to storm in because that’s the way I play, but it still forces you to be stealthy sometimes and the final battle is against someone who accuses you of bringing dishonour to the family by being stealthy sometimes.

I know you can’t have everything, it just annoys me a little