How did that never come up during elections? Mullah party didn't beat the drums?
Why should it come up? Most Pakistanis including the "mullah party" accept that Shias are Muslim; it is only a fringe that rejects them.
The "mullah" parties in Pakistan have always accepted that Shias are Muslim. Indeed, the main religious alliance that formed to oppose Musharraf, the MMA, consisted of both sunni and shia parties.
By the way, Yahya Khan, the ex-military dictator, was Shia too.
Between Yahya Khan, Zufikar Ali Bhutto, Benazir and now Zardari, for almost half of Pakistan's existence either the Prime Minister or the President has been Shia - sectarianism has no place in mainstream Pakistani politics.