I don't think anybody is suggesting that Alphinaud or Alisae are 'evil'.
That doesn't mean they're incapable of being manipulated or simply making a poor choice that causes problems later down the line. In Alphinaud's case that already happened. He learned from it, though.
Previous Final Fantasy games have had protagonists do things that ended up being the wrong decision to make. It led to some pretty memorable moments - and it's certainly a lot more interesting than having the protagonists always pick the right plan and have everything work out perfectly in their favour.
I imagine it will be a theme explored during the upcoming expansion, though not necessarily with Alphinaud and Alisae.