There's no real reason to assume the pilot is dead.
Discovery was right there to beam her aboard. Also, somebody piloted that shuttle back at the end of the episode.
Lorca is a cold bastard, but he's not at the level of randomly offing Starfleet personal for giggles.
This is more sloppy storytelling than the Discovery crew being evil bastards for the sake of being evil.
On the other hand, the augment virus was a terrible retcon that didn't even make a lot of sense, and Roddenberry didn't feel like he had to offer even a hint of explanation when he redesigned the entire Klingon culture and appearance.The "Klingons": Now they could have used the augment virus or anything to explain why these Klingons want a more pure Klingon race but nope nothing and these things act like no Klingons we ever met before they have no honor IMO.