Maybe consider that they took the lives of thousands of innocent unarmed citizens with absolutely no way to defend themselves or means to avoid being murdered. They were hopelessly trapped by the murderers. I think you can safely call that cowardly.
Main Entry: cow·ard
Pronunciation: 'kau(-&)rd
Function: noun
Etymology: Middle English, from Old French coart, from coe tail, from Latin cauda
Date: 13th century
: one who shows disgraceful fear or timidity
- coward adjective
from m-w.com. i don't think you can safely call their actions cowardly. you can call them horrible, despicable, and dishonorable, but not cowardly. it is not clear from the reasons you just gave that the hijackers showed fear or timidity.