IMO, as long as the terrorists maintains popular support of the region they inhabit, it will retain all of its strategic advantages like mobility, invisibility, and legitimacy in its own eyes and the eyes of the people. So long as this is the scenario, these motherfukkers will be very difficult to defeat.
A heavy-handed and indiscriminate approach that could result in significant collateral damage may not be advisable for this will alienate the populace of the region and lay the seeds of later conflict.
However, a heavy-handed pin point accurate approach with minimal to zero collateral damage like, having a reliable intelligence gathering unit capable of infiltrating the most remote ares of the archipelago, assasination of high level financers, symphatizers and supporters of these terrorists, shock and awe assault of terrorists camps to demoralize and mow down their ranks.
The government has to assert its authority over the country and tackle the social issues, like corruption, bad governance, and poverty. It is also imperative to pass laws that are extremely tough on terrorism and any acts of destabilization.
It is a very complicated balancing act, you wouldn't want to be perceived as a tyrant, but also, you wouldn't want to be perceived as weak and meek. Great leaders and governments are able to balance them perfectly.
... 
... 
way.
their women.