It is an unusual legacy for Fretilin to continue to be viewed as being the divisive face of Timorese politics (largely on the basis of the events surrounding the social and political collapse of 2006).
Two of the primary factors leading up to that collapse were the Fretilin government’s decision in early 2005 that religious education in schools would be voluntary rather than mandatory, and the dissension within the military that led by late 2005 to a "strike" by (if I recall correctly) about 400 soldiers. The Catholic church's 19-day shut-down of Dili's main waterfront thoroughfare in April 2005 was a critical spark for what was to follow.
What were the divisive tendencies? Primarily, they were President Xanana Gusmao’s speech to the soldiers that fanned their opposition to the Fretilin government, particularly once Prime Minister Mari Alkatiri took what may have been the only tenable step by that time and sacked them, and President Gusmao's appearance on the platform of the Catholic blockade under such signs as "Alkatiri comunista", as the church’s leadership trucked in hundreds of people to swell the protest and demand Alkatiri’s removal (and mandate Catholic education in government schools).
Standing behind the President at the church’s anti-government rally was the government’s Foreign Affairs minister, Dr Ramos Horta, who didn’t resign until the forces against Alkatiri had better rallied more than a year later.
President Gusmao (between adult Jesus and Mary) and Foreign Minister Ramos Horta (second right from baby Jesus) on the platform of the Catholic Church’s call for the removal of Prime Minister Alkatiri and implementation of mandatory Catholic education in government schools (R Johnson: April 28, 2005).