In the Gita, Krishna is not telling Arjuna to kill his cousins for not having the correct belief in the only true god. Krishna is telling Arjuna to fight, because he has a duty to preserve Dharma. Now Dharma is not "the correct religion", but righteousness itself.
Islam defines righteousness in terms of whether or not its own claims are accepted. Thus, Kafirs are, by definition, unrighteous. They may be very good individuals, but unless they accept that Allah is the only God and Muhammad is his final prophet, they are Najis - unclean - and ought to be converted to the only true religion.
Correspondingly, even a downright thug and a rogue is Halal, as long as he affirms belief in Allah and Muhammad.
Thus, Islam overturns the normal definitions of right and wrong, and then, acting in this strange context, deems it right to punish Kafirs for their unbelief.
Krishna and the Gita do not do that. It is righteousness that is important, not belief in some god.
