Yes, the KLA utilized terrorism, which qualifies them for inclusion in the 'terrorist organization' category unless it can be proven that the leadership had nothing to do with those acts - yeah, right.
But they are less of a terrorist organization than Milosevic et al, which puts them in the same boat as Rashid Dostum and various other Afghan warlords who became allies of convenience in efforts to address larger problems and who are now being pressured into conforming to civilized norms.