Is transporting the deceased father of a friend from outside Mecca to Mecca, praying over him, and burying him there, three hours after his death, considered harming the deceased or a forbidden act?

There is no harm in transporting the deceased for burial in Mecca. Rather, his son has done well by transporting him, as it is the purest of lands and the most beloved to Allah. Some jurists have even recommended transporting the deceased for burial there. The prohibition of transport applies when there is no overriding valid reason, while it is recommended when it is to a virtuous place, such as Imam Shafi'i's recommendation to transport the deceased to a virtuous land like Mecca.