You are right, he cant do anything explicitly against minorities.....but then he didn't do anything explicitly against muslims during Godhra too. He just turned a blind eye, which cost thousands of musims there life.
And since he can't do anything against muslims, he will try to ignore them, which, itself, is a very dangerous proposition given the dangerous paths of communal peace the Indian Democracy balances and survives on....
You can be guilty of a crime by inaction just as much as by action
Maybe Modi did what he did. But today Ashoka who killed thousands in the Kalinga war has his emblem on the flag, currency, passport and what not.
I think Indian history judges people by the net of good and bad.
Well that just about says it all