Assume that what Malala tells us about her father's description of the conflict between the USSR (now Russia) and the US in Pakistan is accurate. Did the people making decisions about American and Soviet activists in Pakistan act in compliance with or in violation of Utilitarianism? Did they act in compliance with or in violation of Deontology? Were they acting virtuously or viciously?

Your question is an interesting one! From what I can see, the novel doesn't mention American and Soviet activists in regards to the conflict between the USSR and the United States.
It does, however, mention how the American military and intelligence apparatus approached the Soviet invasion of Afghanistan. Essentially, the Americans saw the Middle East as an invasion they should fight in order to keep that part of the world and its resources free of Communist influence.
Meanwhile, the Soviet power structure (both military and intelligence) viewed its takeover of Afghanistan as a strategic move against the Americans. The Soviets subscribed to what they called the Brezhnev Doctrine, which held that once a country embraced socialism, it could never be permitted to return to capitalism.
According to Malala's father, the Soviet invasion of Afghanistan came during the reign of General Zia in Pakistan. General Zia came into power through brutal means. He had the country's then prime minister, Zulfikar Ali Bhutto, arrested and hanged. General Zia was largely unpopular with the international community, especially after he instituted a program of Islamization in Pakistan. In response to General Zia's reign, the power structure in America voted to cut off aid.
Everything changed when the Soviets invaded Afghanistan, however. Then, billions of dollars in aid and weapons were sent to Pakistan. The goal was to help General Zia's ISI (the Pakistani intelligence apparatus) train local Afghans to fight the Communist Soviet threat. Under General Zia, the idea of jihad became a core belief promulgated by both the Pakistani and American power structures.
Malala's father maintains that the CIA supported the idea of jihad against the Soviets in Afghanistan. The Americans were willing to work with a blood-thirsty dictator (Zia) to defeat the Soviets.
So, did this unusual partnership between the American and Pakistani power structures adhere to Deontological or Utilitarian ethics?
By all indications, the partnership supported the Utilitarian concept rather than the Deontological one. The Utilitarian ideology is based on the idea of acting to benefit as many people as possible. It isn't based on a set of rules or a moral code, whereas Deontology is.
So, in this case, the American power structure decided to choose the lesser of two evils (the Utilitarian approach), rationalizing that the partnership with Pakistan (and General Zia) would save the Middle East from Communist infiltration and oppression.
In the USSR, the Soviet power structure initially ruled out sending Russian troops to Afghanistan. However, it soon reversed course after the prospect of an Islamist takeover of the Communist Afghani government became increasingly likely. Russian soldiers were thus sent to Afghanistan to quell the Islamist uprising from succeeding.
So, there you have it. Both the American and Soviet power structures made decisions that affected millions of civilians. These decisions were based on Utilitarian rather than Deontological ethics. Both sides were looking for outcomes that they thought would benefit the majority of the population in their respective parts of the world.
http://www.understandingwar.org/russia-and-afghanistan

https://history.state.gov/milestones/1977-1980/soviet-invasion-afghanistan