Perhaps you don't really have a handle on the mechanism of operation here.
Its not about # of deaths, its about amount of terror (government over-reaction in response to politically motivated violence).
Wars were started over a little over 3000 deaths on 9/11.
Flu virus just doesn't have the effect.
OK, you are right, nobody will be scared because of flu even if it's more effective, however as Ebola isn't very easy to transmit in a well developed country a few terrorists can cause only very limited issues what the government can easily cover up. Certainly if the govt already want to impose martial law for it's own advantage then these guys would be the perfect cause.