You want to down rep someone into being a super villain?

No,they have (dereppers) done it to me.

protoype 2 mercer being villain, stopped me from playing the game, since its totally beats the purpose of first game and that dude didnt fit the villain type formula

You still have 37 rep so the world is safe for now.

Drakengard does that. It helps that the main character of the first game is a murderous, blood-crazed psychopath as a parody of the traditional JRPG protagonist.

Of course it will work. Depends on the execution, it will make an interesting plot twist.

Well, if you want to do it the easy way, the protagonist can just become the faux villain of the sequel. Meaning the former protagonist are not the true villain. He/she just looks like a villain now because you see it from different POV, or just controlled/brainwashed by the true villain all along ! In the end, they are still one of the good guys :)
Ex : Dante in the Devil May Cry 4, Richter Belmont in Symphony of the Night.

But you can also going all out and make the protagonist the real big bad of the sequel. In my opinion, if you want to make this kind of plot work nicely you will need :

1) A hint, from the previous game that explain why this change are possible. It can be very subtle, but undeniable. Fail to do so, and the player will fell the change are to sudden or out of character.

2) Somehow you must make sure the player can sympathize the fallen protagonist cause. Maybe the protagonist think he/she do it for the greater good. A necessary evil. Or he start slaughtering people because in this universe the humans are bastard. Or his former hero team/guild betray the protagonist first. Whatever the cause, what he/she doing now as a villain are too extreme and there is no turning back. That's why we need a new hero now.

There are other ways too, like in Diablo series. In the Diablo II, All playable character from the first game are corrupted, one of them even become the Diablo himself. It's not that they become villain of their own will. It's just the true villain are too powerful, and he even successfully corrupt all the former hero. It's a nice way to show the horror and power of the true villain.

There are trope of this on TV Tropes if anybody interested to read it :D
it's here :

http://tvtropes.org/pmwiki/pmwiki.php/Main/RogueProtagonist

By the way, adding Castlevania - Lords of Shadow series to the list of game where the main character, became the main villain of the next game.

Castlevania Symphony of the Knight. Dark Priest Shaft possesses one Belmont clan member and makes him temporary lord of the castle.

I won't hold back on these turds.