You don't understand how this light/dark thing works, or you're just not expressing it well.
It's not evil versus benevolence.
Dark is the direct path. It gets associated with things like greed and zealousness and malevolence and other negative thoughts and emotions only by virtue of the fact that those kinds of people are generally the kind of people who prefer the direct and straightforward power.
Light is working around everything, manipulating the flow of things, working THROUGH yourself and others. A more convoluted but arguably more gratifying path with, also arguably, somewhat greater potential.
Negi wants to protect everybody. Being dark doesn't mean he can't work well with his team like a light mage would though, but it means that his way of using them will be different for sure.
tl;dr what I'm getting at here is that being dark doesn't mean he won't be a goodie goodie or a team player anymore.