Rule by Congress probably would have CAUSED radicalization. Just as the establishment of the Jewish homeland in Palestine in the Palestinian Mandate caused Arab resistance to Jewish immigration. The Muslims would have immediately started to demand inclusion in the government, and if the Hindi majority has resisted, as they probably would, then no telling what might have happened. The differences may superficially seem to be like that French-Anglo divide in Canada. But I think that it would eventually have followed the route taken in the Palestinian movement where religious fanaticism begins to grow and grow and to make compromises almost impossible. The British would have been caught in the Middle.
2. Muslims were already represented in the Congress -- Maulana Azad etc. and they stayed there even after Pakistan was created. There were also pacifist Moslems like the "frontier Gandhi" - a Pathan (from the north-west frontier province): Khan Abdul Gaffar Khan.
3. Though the rest of your point about a growing fanaticism rings true - Hindus in the 1800s welcomed the British for having destroyed the possibility of Moslem rule (even the current Hindu rightwing RSS did not participate in the national movement)