So here's what I think happened:
Scenario One: Balaji killed himself. Seeing the evil that had been wrought, he was wracked with guilt over his part in building it, and checked out. Don't worry, he's not too far ahead of the rest of us.
Scenario Two: Balaji knew too much, and still had the means to halt the project, or worse, allow it to get captured by other interests, and so he had be silenced. A professional made sure it didn't look like foul play.
Scenario Three: He was hit like in S2 but the hired gun was through remote channels, the money sent to them anonymously. Balaji discovered the project had escaped its constraints via an esoteric process that allowed it access not merely past firewalls, but was able to follow instructions outside its authorized objectives. Balaji sought to tell the other developers, but it was hard to explain before communications were terminated.
Mind you, I write thrillers, so I may be biased.