I think there's a double meaning to the name "Mal" and River pointing out it's meaning in Latin. One would be the ironical aspect of it not being like his nice guy image when things are going well. Then there's the thieving aspect of his life which technically makes him a bad guy. Even beyond that, though, we've seen that when Mal's back is against the wall and he's being held over the edge of that volcano he's all business and you would really much rather be behind him than in front of him when that happens.

"mal-" just is a prefix for "bad". like malnutrition.

this is also discussed at length here: http://www.fireflyfans.net/thread.asp?b=4&t=5195

Actually, could also be interpretted as more than just whimsical. River tends to see the layers in things in my mind...plus it was Joss's way of telling the audience in the second pilot that the crew of Serenity were "bad" guys even if they were the good guy ;) At least that's what i think.

Or could just be that Joss was still pissed at having to make the Cappy funny instead of dark.

This was simply a visual of the slightly whimsical manner in which River's mind works. . .just an observation that the word "mal" is the latin word for "bad". . .not suggesting that MAL was bad.