When you read Nixon's writings on foreign policy from around that time, especially Asia after Viet Nam (1), he was still very much thinking in terms of potential communist expansion in South and East Asia. Men like Pakistani president Yahya Khan were useful in their ability to suppress communism. It would be too simplistic to say that Khan was forgiven for his crimes by virtue of being a foil for communism in the region though. The primary concern for the Nixon administration was that Yahya Khan was a key part of opening up China.
The geopolitial situation in the area was incredibly precarious. China and the Soviet Union had been drifting apart for years, to the point of brief outbursts of open hostility, essentially ever since Stalin died. China considered Mao to be the final authority on communist ideology now, especially in Asia, which Russia refused to acknowledge. China also refused to accept Russian meddling in neighbouring countries like Vietnam and Korea. It also believed that Russia was dragging its feet on giving China the economic and military support it needed to reach its full potential. Nixon and Kissinger hoped to use this Sino-Soviet Split to their advantage by setting up a diplomatic triangle in which they could play out the Soviet Union and China against each other. Raising China to the status of diplomatic equal to the Soviet Union would mean that the communist world no longer spoke with one voice.
With this split going on China had formal diplomatic relations with Pakistan, which eventually allowed for the aforementioned opening up of diplomacy between China and the United States which Nixon back in 1967 accepted as necessary for long term global peace and stability. Meanwhile over on the Soviet side, India had signed the Indo-Soviet Treaty of Friendship and Cooperation, which seemed to signal the end of India's neutrality in the Cold War. By all accounts Nixon took Indira Gandhi's involvement in the Bangladesh matter highly personal. It threatened to turn the Bangladeshi Liberation War into a proxy war between the Soviet Union and China. Perhaps most tellingly, the Warsaw Pact countries were among the first to recognize independent Bangladesh, China was one of the last.
So the short answer is - Nixon was more concerned with his long term plans, opening up a formal relationship with China, which he couldn't do without the support of Pakistan in general and Yahya Khan in particular. Nixon needed that relationship with China, both to weaken the bargaining position of the Soviet Union in world politics and because China was very close to becoming a nuclear power.
(1) Richard Nixon, "Asia After Viet Nam." Foreign Policy Magazine, 111(1967-1968): 111-125.
Further reading:
Lorenz M. Lüthi, The Sino-Soviet Split: Cold War in the Communist World (Princeton University Press, 2008).
Kalyani Shankar, Nixon, Indira and India: Politics and Beyond (Macmillan, 2010).