The deployment of 2,700 foreign peacekeepers helped restore order, but tensions have flared in recent weeks, raising fears the country's presidential elections, due in April, could be hit by violence.
Although no-one was injured in the attacks on homes belonging to Gusmao's family, the violence marks a shift in the country's political landscape.
Gusmao was widely regarded as a hero for leading East Timor's struggle for independence from Indonesia.
But dissatisfaction over the country's lack of progress since independence has led to growing criticism of his presidency.
That anger has grown since Gusmao ordered Australian troops to raid Reinado's hideout in the mountain village of Same, south of Dili early on Sunday.
Reinado was jailed last year for leading a mutiny with nearly 600 soldiers and deserting East Timor's armed forces.
The mutiny triggered clashes between rival factions of the security forces and led to the worst violence seen in East Timor since its bloody break from Indonesia in 1999.
He escaped from prison in September along with 50 other inmates.