From what I heard Akamatsu was presumably forced to hastily end Negima out of protest over a proposed law granting publishers, editors, etc. rights over any work co-created with the author. Should it pass, there's a risk of abuse, including reduction of the author's rights over his/her work, or even going after second-hand works (fan art, doujinshi, etc.) without author approval. With Kodansha (Akamatsu's publisher of choice) supporting the proposal, Akamatsu has naturally no intent of renewing his contract.