I think it's a shame if he and RTD aren't on speaking terms, since the first series was the best one too date IMO, and Second Coming (another RTD/CE project) was amazing.
If you think about the situation from the perspective of an 'regular' job like mine and yours (!), then your current employer telling all the clients, suppliers etc that you're leaving (and for false reasons) before you've had a change to explain it yourself is pretty shit behaviour. In the context of acting (and when integrity and reliability must be one of the fundamental requirements in what seems to me to be a fickle business), then the BBC really did **** it up as the press release could damaging to his career.
I think it's a real shame - I've always thought that Christopher Eccleston, along with his contemporaries such as Ewan McGregor, Daniel Craig stand head and shoulders above other actors in terms of talent and I hope that whatever this problem is, doesn't prevent him from returning to the small screen. Ultimately it's all the fans that he found through Doctor Who who are being short changed at the moment, and that's sad.
And yeah, I wish he was returning for a cameo... or entire series 5,6,7,8....