Nearly every single evil person in the history of mankind had rationalized their actions as being for "good". I know Hitler did it, and many other oppressive regimes did it too. I'm sure MIB is doing it as well. He seems to feel that he is unfairly trapped by Jacob and "just wants to go home." Hell, ET just wanted to go home and he wasn't evil.
However, "Many of the truthes we cling to, depend greatly on our own point of view." - Obi-Wan Kenobi.
I'm sure from MIB's point of view, he is not doing anything evil, but if Widmore is telling the truth and it will result in everyone ceasing to be, then objectively speaking, that would be considered pretty evil. Even if it is a completely seperate timeline, destroying an entire universe would be beyond genocide.