Well, that's honestly down to the player for the most part. It's still a sandbox and we are free to play MC as we want. Sploosh actually even talked about cleaning up the main story at some point, so MC wouldn't have to fuck anybody to solve it, if that's what the player wants.
Their goal, as stated, is to enable "true one girl routes" for the main girls, if the player choses to take them. You just have to keep in mind that about 50% of the playerbase, among them for example quite a few people here (looking at
srksrk 68), want to be able to get as many girls as possible - or even all of them - in one playthrough.
There's simply a limit as to how far DC will be able to make everbody happy. It's an immanent problem, simply because there are just so many chracters. The only way to really solve it would be to add strict routes, so MC can be consistent within that route without ways for the player to switch into another scenario. But as said, that's not what's on the menue.
Those who really want total consistency will likely have to play real VNs or kinetic novels - SS will probably never reach that level.