Not being able to talk to NPCs or allies, and NPCs not responding to being attacked is a bug. It doesn't matter if someone triggered it by screwing around in a manner you don't approve of.
This particular issue probably isn't going to take up any of Larian's time, unless it reoccurs after the next update (being likely related to the issue of killing Egleander or talking to Desdemona, and changes happening with NPC AI WRT hostile actions).
The consequence of designing the game to be able to kill NPCs is that there are multiple ways to get quests, multiple solutions, and the game should react properly to co-op players doing different things if they split up. That gives you the freedom to go exploring and get a quest before even finding a particular NPC, even if they are alive and well and you have no intention of changing that.
If Larian were to have decided a few years ago to protect main plot characters from being killed, the resources freed up by that simplification were still never going to be put into an entire lumberjack simulator, complete with learning the relevant skill(s) from quests rather than something so common as skill points.
