I don' think any of what happened in the hatch was planned. I think he's willing to do anything to get Jack and co. to go after the Others and when he found out they had one of them locked up, and the whole situation with Ana he saw a chance to use it to his advantage by framing Henry for killing Ana and shooting him<when Libby came from behind he was pretty much caught by surprise and just turned and shot>
Now the question is, once the initial shock of what happened passes, how is Michael going to explain how Henry got out to begin with, and got Ana's gun and shot her without her moving from where she was sitting, unless he takes the time to move her to a different position.