^I can confirm that the Knight killed a Civilian thing (as well as still getting the prize despite it) did happen, and there's absolutely no way of preventing it other than hoping he'd miss the attack.
I'm in Chapter 19 now, so some notes (apology if you're already aware of most/all of this):
-The skill Vantage is bugged. If the condition (attack first if HP<50%) is fulfilled but the user has no way to counter (either because the opponent uses ranged weapon or that the user uses something like Firesweep Sword), the game would freeze. This could get really annoying at times, as you have to kill enemy Swordmasters with melee instead of ranged and therefore have to eat their attack first for no good reason at all.
-Marisa and Knoll are not playable (they don't appear in the unit selection menu after you got them in their respective recruitment chapter). Not sure if this is intentional or not, if it is, they should just be omitted from the story altogether
-I can't save normally, which means I had to rely on save states a lot. For reference, I'm playing on VBA with Flash 64K Save Type.
Otherwise, I'm having a good time. The Sacred Stones that allows you to play both routes always felt like the ideal version of the game to me, and I'm enjoying using the new characters too (I assume at some point they'll get their custom portraits/mugs?). This is also the first time I play the game with the Skills system, and it does add interesting new wrinkles to the game, other than the Vantage annoyance. I'd gladly replay this if the more polished version comes out in the future, hopefully enabling the Iron Man playthrough, which seems a great fit for the hack's large roster selection. Thank you and good luck.