There is NO WAY in the universe that Bowmer quit. He has been Mr. Ames' right-hand-man since the beginning.
What's far more likely is that he got caught saying something less than flattering about Meredith, McNair or Ceiseilka and a spy turned him in.
They way they do it at LCG HQ's is they sit you down at the executive table and tell you that you are fired but if you agree to sign a series of papers relinquishing your rights and stating that you will remain silent, they will go with whatever reason you prefer (quit, needed to move to take care of mom, had health issues, etc.).
This is how it has always worked at LCG headquarters.
Bill and John were fired from editorial no matter what lies/spin HQs tries to spew out.
The only question that remains is why?