Yes, at the Indonesian embassy i Kuala Lumpur you can get a visa too, bring it in the morning (09:00-12:00) and pick it up the next day in the afternoon. Bring a return ticket either on bringing or picking up your passport!
Don't know about the services of VoA at Banda Aceh.. I can't find the airport in the lists on several websites, but will you be denied boarding when going to Banda Aceh without a visa? That would be strange.. you should ask that at the Indonesian embassy in Kuala Lumpur first, just to be sure. If not, you apply there right away, right? VoA is cheaper dan applying for one on beforehand.