Dr. Light isn't evil simply because he isn't the instigator, Wily is.
Wily is the one that starts new things, that is the archetype for a villian, such as Satan or Loki. Dr. Light did what he did at first within acceptable parameters. Wily endangered the lives of civilians and Dr. Light responded in a way that had to equal Wily's. Fight fire with fire as they say.
As Jung or Freud put it ( I can't remember which of the two, and I'm only paraphrasing) you cannot deal with evil without risking evil becoming a part of you. Yes, Dr. Light did knowingly pressed on when he knew the outcomes would most likely be violent, but it was always when reacting to something Wily did first.
To close I will quote Dr. Light from Maverick Hunter X.
"My name is Thomas Light, I am the researcher who designed and built Mega Man X. I granted X special powers that no other robot posesses, utilizing he conscious, he is able to think, worry, and act entirely of his own accord. This means that he is also imbued with the materials necessary to facilitate the evolution of robots in the same matter as light/life (not sure which.) It is an unfortunate fact that human life is short and fleeting. I fear that I will not have the time to ensure the safety of the X Project, that is why I have decided to seal him away. Perhaps he will be discovered in the far flung future, and will fight valiently to ensure peace for all people. Yes, I firmly believe that this will come to pass, but I am not without worry, I fear that X will be swept up in the war we call progress. I urge the people of the future, to remember that X is my, nay, the world's hope."
The wars were inevitable. Dr. Light was just participating the best way he knew how.