The Muslims rulers were also not very different from the Politicians of our days. Once having established, they were only interested in amassing wealth, filling up their harems with beautiful women, constructing monuments, etc. They did not care for the common muslims. If they had cared, there was no need for "Sachar Committee" and things like that.
As in any turmoil anywhere in the world, the vicitims of the actocities committed by the Islamic invaders were the poorest of poor and indefensible natives of India. Most of the converts were from the lower castes of the native religions and as such the condition of Muslims in India is also not better than the "dalits" and other lower castes of other religions.
There is no need for the Muslims in present day India to justify the atrocities committed by the Invaders. You (or your anecestors) were the victims of their atrocities.