What are the disadvantages of forbidding flights to and from the African Ebola region?
I think the disadvantages are mostly economical in that region and so they has nothing to do with epidemiology. Possibly a long term effect can be, that the economy of the region turns from bad to worse, which can affect the healthcare too, but that's just speculation.

The advantages are obvious, ebola is quarantined at some level, so these measures prevent or at least slow down its spread around the world.