No, you're right. Meta Knight is depicted as having honor and good intentions. He and Kirby are usually at odds, but I wouldn't say Meta Knight is bad or evil at all. He fights for the good of Dream Land, same as Kirby. And whenever he and Kirby duel, Meta Knight honorably leaves a sword for Kirby to defend himself.
I think where you get it wrong is the "evil rebellion" part. I don't see anything in the update about an evil rebellion. All I see is that Mario and Kirby decide not to fight, i.e. disobeying the rules, and have to deal with the consequences. The Halberd's part in that is unknown.