My personal opinion is that Mata Nui already IS evil; presumably he didn't go rampaging around showing this for the same reason Makuta doesn't smash the Mangai- it's his place. However, he may wake up on the wrong side of the bed and/or be angry at the Matoran for letting the Brotherhood get the best of him and/or become paranoid and institute a big nasty distopia so that he doesn't get challenged again.
HOWEVER, I have very little basis for this. It stems entirely from reading that after writing my story Elder Brother, along with the fact that I think it would be awesome. (hey, I'm a Dark Hunter, right?)
There's just something in the way they say "allowed to reawaken" that gives me an ominous feeling. I'm just not sure why...
—Dark Hunter Lewagirl