Bill Howard tells us more about his decision to step down in this article by Andy Baggot. He admits that he and Eaves could have parted on better terms, but he is clear that he was not pushed out. He says he wasn't enjoying what he was doing as much anymore and that it just felt like the right time to step down. He maintains that the decision was his alone.
I'm sure part of the reason he wasn't enjoying himself as much was conflict with Eaves, but that's not much of a surprise. I'm still sad that Howard is gone, but I don't feel quite as bad about the situation anymore.