Lore Question about Heinrix (end of Chapter 4)

Hey all, I'm new to the 40k lore and some things I have trouble understanding even after reading wikies and forums regarding the subject, so could someone clarify Heinrix's decision for me please?

On my 1st run I:

  • ended up being a Dogmatic-2/Iconoclast-3 mix
  • spent the whole game on the best terms with the Inquisition
  • romanced Heinrix

After the Tech-priests world in Chapter 4 Heinrix decides that the Inquisition can go to hell and that he quits. While I understand and fully support his desire to quit, couldn't it have been done in a way that would not brand him "a traitor and a heretic" and make him a very likely target for assassination? From what I gathered from the forums, Inquisition members are allowed to retire? Couldn't my RT use her influence or make a deal with the Inquisition to let him go? This all felt out of blue and left me very confused (especially considering that at that point we didn't even know what Lord Inquisitor was doing exactly).