Welcome to the forums. I'm sorry to read your story.
It's hard to be able to give good advice since it depends on where you are and where you want to go. In general I agree with Hedge, that Head of the Department might be able to help with the letters of reference... the "easier way out for everyone" i.e. a good letter for you and a non-confrontational deal for them might be in the best interest of all?
However,there is always situations. You state you were his first graduate student, that explains a bit of the situation, and the non tenure track position. That might explain things if you state that in combination to the letter- but not the best of places to be for you.
I would agree thought that in order to "survive" in science you need more than heart and love for science. There is that politics aspect that makes the grants, publishes the papers and (imho) is as important (or relevant might be a better word) as the actual science done at the bench today... I don't like it, but as far as I've seen it - that's the reality.
And I do think, considering what I went through during my graduate years, you need to remember that noone will "help" you but it's more of an exchange of favors and "doing the right thing which leads to the least hard time for the people involved". It might require a bit of swallowing pride or sense of fairness, since it isn't fair per se, but to look out for what will end best for you.
All the best!
"One never notices what has been done, one can only see what remains to be done" Marie Curie