The president's pardon power is limited to federal offenses; the Constitution only grants the president the power to pardon "[o]ffenses against the United States." An offense that violates state law, but not federal law, is an offense against that state rather than an offense against the United States.
The rebellion was the result of decades of ethnic and cultural differences between Indian soldiers and their British officers. The indifference of the British towards Indian rulers like the Mughals and ex- Peshwas and the annexation of Oudh were political factors triggering dissent amongst Indians.