For the Heart of the White March quest, turning the gem over to the Crucible Knights or the Dozens was originally a part of the game (those journal updates appear in the data files) but it was cut from the final game, probably due to not having enough time to write a whole "House Doemenel gets angry and tries to kill you while the CKs/Dozens have some more unique lines" thing.
And for your thing about the research, there is a limit as to how much non-linearity you can go with the game. "No, Lord Raedric, I will only kill Kolsc if you give me half your kingdom! No? Ok, a third. Still no? Ok - my last and final offer, a quarter? Alright then, I want the land with the best cattle grazing, and the most villages........"