Historically, we have dealt with belligerent non-sovereigns (e.g. pirates) via the military. How do you think treating Al Qaeda as a military threat has corrupted the military? My great worry is that if terrorism is treated as a crime, then the protections available to all accused criminals will be watered down to accommodate the needs of prosecuting terrorists. That's what, e.g., has happened in the drug war. There are a lot of bad doctrines (e.g. no-knock warrants) that were motivated by the drug war (specifically the ease of concealing or destroying evidence of drugs).