From a humanistic point of view, you are perfectly right. Even, undue loss of one human life is crime. Rape, in any case, is totally unacceptable and dastardly act. Though not relevant, but I consider all those Bengali women as my own sisters, who unfortunately have to go through this ordeal owing to criminal acts of certain Pakistani elements, whether from army or otherwise.
But, you must realize that Pakistan was carrying out a counter insurgency operation in East Pakistan, believing and thinking that it is integral part of Pakistan. There is hardly any example, in history, where atrocities were not committed in the counter insurgency operations, from either sides, more so from the state side. One reason is that generally, under such circumstances, established law and order declines and law enforcing agencies are granted extraordinary powers, which they sometimes misuse. This is a hard fact of politics and there is hardly any exception to it.
Numbers become important, not from a humanistic point of view, but from practical point of view, to establish, whether the state forces were using undue force and means to curb the insurgency. For example, if one accepts the figure of 26,000 civilian casualties, in a counter insurgency operation, extended over a period of 6 months, against the potent force of Mukti Bahni; no sane person would declare it undue or term it genocide.
Having said all that I have said, I am of the view that the counter insurgency operation, carried out by Pakistan, in March 1971 and onward, was totally unjustified and a gross blunder, which then Pakistan had to pay for with the surrender of its forces and its aftermath. In my view, after the break down of talk between Bhutto and Sheikh Mujeeb, in March 1971, and their failure to arrive at an agreed constitutional framework, Pakistan, on its own, shall have, by mutual consent, given East Pakistan its due liberation and brought its whole state machinery, back to Pakistan, under an agreed arrangement. That was the real solution; but General Yahya did't had the courage and guts to implement this logical and sane solution.