From what's been written in a few behind the scenes accounts, it was always planned for Christopher Ecclseston to be in 1 series, then regenerate, kind of as an introduction to the new fans of the concept. But the story leaked, and the BBC being a public broadcaster weren't allowed to lie when directly asked if he was leaving. So it was confirmed, and because of the rush to get the story out before the tabloids the article was badly worded and implied Chris couldn't hack the work load, which he (his people) took execption to, the BBC later apologized for it.