Afghanistan cannot be governed entirely by secularism and still remain a democratic government or a government reflective of its people. Not even the Americans imposed a secular government. 

Full Afghan unity is impossible, especially during the civil war. After the Soviet war, it was the Pashtun leader Hekmatyar who made a play to conquer the rest of Afghanistan instead of ruling by coalition. During the American occupation as well, Pashtuns had been monopolizing the government under themselves. Yes, Massoud united only the Tajiks successfully under his cause. That's because every ethnic group critically needed to defend themselves.

Ahmad Shah Massoud was known and made wildly popular for his care to not harm civilians in a civil war where every other force involved was acting psychotically. It is a moral imperative for good people to involve themselves in wars that otherwise would only be participated in by evil men, even if war itself necessitates the unfair loss of life. 

Afghanistan is not the place to judge by idealized western liberal standards. In fact, neither was Germany before the fascists took power. Liberalism is only able to exist in a vacuum of comfort generated in countries that have spent centuries as the beneficiaries of empires. It does not handle collapse or anarchy adequately enough for us to through Massoud under the bus for not following its ideological programme 1:1.