Autofocus on video DSLRs sucks. Period. You should not use it, basically ever. Especially on a green screen shoot! If it hunts for focus in the middle of your shot, you're going to have trouble with the key separation, and it could potentially ruin your shot.
Also, the 8-bit 4:2:0 h.264 is not going to lend itself to good keying anyway. So you need to focus manually to ensure you have control of your results--get a follow focus, or hire an experienced focus puller. Don't let autofocus ruin this for you!