Like it or not, there is an inherent morality built into the Star Wars universe. Certain things are good, certain things are bad. As far as the strain penalty is concerned, it's probably the best mechanical means to show what must be the obvious stress of holding on to anger, hatred, and rage, three things we know cause stress (and therefore strain) in real life. And as far as a wound bonus for Light Side goes (I was under the impression it was a strain bonus, but whatever), we all know that when people perform selfless deeds, they often have bursts of adrenaline and can do more than they normally do.
Also... if you don't like it, remove it at your table. All the rules are only suggestions, anyway.