It may not seem to be in our interest to have to deal with many
possible new states down south, but it is a less terrible deal than
for e.g, an Aceh that has escalation of violence and the possible
entrance of foreign militants that take advantage of that political
standoff and use Aceh as a battleground to spread their cause for
an Islamic Khalifa through violence and coercion.
By empowering the local Aceh nationalists, you give them the power
and the standing to ensure that they will attempt to maintain the
gift of autonomy that they have given. Consequently, it may be
easier to invest in such a region, because they have more control
over their natural resources too.
Furthermore, the Acehnese have always been at odds with the
Javanese, same as the case of Timor Leste, which apart from
Indonesian annexation in the 70s, did not share a single culture
nor ethnic history with the ruling elites in Java.