Although the Final Report of the Special Commission has never been made public, Sarshar (2017) and Hull (2012) highlight a variety of reasons that were discussed at the time, which were as political and ideological as strategic and practical.
First, it may be of interest to note that there were in fact two earlier proposals which would have established the capital in or near Karachi instead (Hull 2012, pp. 36-37). The first from 1947 was criticized, somewhat ironically, for placing the capital too far (20-30 miles) from the existing city. A 1952 proposal would have addressed this by placing the capital right in the center of the city. Initially the primary objection to this plan was that it was too expensive. Ultimately however this report wasn't even published because of the assassination of prime minister Liaquat Ali Khan and resulting political tumult that brought Ayub Khan to power. The opinions of Ayub Khan were clearly central to the ultimate location of the capital away from Karachi, near to (but also separated from) Rawalpindi.
Sarshar (p. 249) quotes Ayub Khan's inaugural address regarding the new capital, highlighting his ideological commitment to building "from scratch":
Whether the capital was to be in Karachi or elsewhere, it would have
had to be built... It must have a colour of its own and character of
its own. And that character is the sum total of the aspirations, the
life and the ambitions of the people of the whole of Pakistan... Our
people, by and large, are tribal by instinct, by history and by their
traditions. With the two provinces of Pakistan, separated as they are
from each other, you want to bring the people on a common platform.
The thing to do was to take them to a new place altogether... It is a
question of binding the people of Pakistan, a question of giving the
right sort of environment where they could produce the best results.
According to Hull (pp. 39-40), newspapers reported that the commission identified the following reasons for the location northeast of Rawalpindi:
The region’s moderate climate and changing seasons would prevent
boredom and lassitude and promote health and administrative
efficiency. Lying on the Grand Trunk road, the site offered advantages
as a center for the region’s economic development. The availability of
cheap rural land would decrease development costs. The geography of
the region and the military base in nearby Rawalpindi gave the site
greater strategic security than the seaside Karachi. Planning from
scratch would allow greater order and beauty; the Commission
reportedly observed that “although Karachi is a relatively modern
city, its development has been unplanned and grotesque. It cannot be
converted into a city of aesthetic beauty—an essential requirement of
Hull immediately goes on to add:
Constantinos Doxiadis, the Greek planner appointed to design the new
city, would soon praise the “typical, characteristic architecture of
the [Rawalpindi] area, growing out of the land, the people and the
climate,” while finding “that of Karachi area... strongly influenced
by Hindu principles” (Doxiadis Associates 1960b:68).
Along similar lines, from Sarshar (p. 255):
In Pakistan, one of the most developed institutions was the army in
Rawalpindi, and the move of the capital served as a consolidation of
civil and military power. Many were of the opinion that Ayub chose
Rawalpindi for this purpose and proximity of the site to his ancestral
village. The preference of the site “answered nearly all the questions
pertaining to climate, landscaping, communications, defence,
availability of building materials, water and power resources and last
but not the least, aesthetic and natural scenic beauty.” The location
was important in the sense of Islamic identity because it was at the
conurbation of Grand Trunk road and added to enhancing the capital’s
importance by proximity.