absolutely he can, but Superman has been shown to have at least some ability to resist mind control if he's aware that it's happening. An example would be his fight with Manchester Black.
as for phasing, no Superman has no protection against phasing, but his organs are just as strong as the rest of him, there isn't a wolverine thing going on here.
So assuming that Martian Manhunter and Superman are at equal physical strength it would be like you trying to rip skin in half, which is rather difficult.
what would be easier would be for Martian Manhunter to simply phase a single part of himself inside of Superman, like a finger, and solidifying it cutting off blood flow to his brain or whatever.
That is of course assuming MM could get close enough to Superman to do so, he has been shown to be able to "wide beam" his heat vision and he's a lot faster than MM, if he runs he'd have a much better chance.
I also don't know if MM can survive in space, which if he can't is a great advantage for Superman