I understood Banda Aceh was under martial law before the quake.
http://www.laksamana.net/vnews.cfm?ncat=48&news_id=7777
You are correct.
Church burnings have been an intermittent occurrence for the past 30 years. (Aceh was a forerunner in the significant increase of attacks on churches that has taken place throughout Indonesia.) The most significant protestant church in Banda Aceh, the capital, was burned down in the early 90's. Subsequently, permission to rebuild was refused.
Local church communities can have great difficulty getting permission to have a place for worship, e.g. having to build over water, or use the back of a shop.
Christians employed as teachers in schools (posted by the state education system) can come under enormous pressures to convert to Islam. Prayer for these isolated Christians is urgently needed.
The potential for conflict is perhaps greatest in South Aceh, where Batak ethnic communities include both Christians and Muslims. Without a clear ethnic-religious alignment, conversion to Christianity does not bring loss of ethnic identity and this can make conversion easier. Consequently, greater pressure could be brought to bear on the Christian community. (This is just my hypothesising about why South Aceh has been a region of conflict.)
Persecution of Christians is sometimes hard to distinguish from persecution of Chinese. During the massacres of "communists" in the 1960's, many Chinese Christians were killed. In Aceh a religious test was sometimes applied: if the person could not recite the Arabic confession of faith in Islam they were put to death. I had this from a Muslim person who narrowly survived the massacres.