Just bumping this because it seems to be the only topic discussing this issue.
I was likewise kind of annoyed that simply accepting the second quest from the Dozens disqualified me from working with the Crucible Knights, even though I have Champion reputation with them. It should definitely be changed so that completing the second quest is what locks you in - either that or giving an option in the respective questlines to betray the Dozens/Knights/Doemenals to a rival faction.
Or at least having it so that if you sink your reputation with a rival faction you can then progress with another one.
It's just annoying that there isn't an option to do *something* about it, especially considering the freedom of choice PoE presents you with in other interactions.
