"What I did, I did without choice. In the name of peace, and sanity."
Based on the words he used, I don't think he was forced to do something against his will. It sounds more like the situation with the star whale in "The Beast Below" where there were only bad solutions and worse solutions. He even said after killing the star whale, he would have to take another name as he wouldn't be The Doctor anymore.
Given that The Beast Below was his second episode after taking over from RTD, does this also imply that Moffat had been planning and laying the groundwork for this 50th anniversary story since 2010?