I don't think Whedon knew exactly how many episodes he'd get. Just that he found out he was getting the axe with enough time to condense a pre-planned wrap up. The war was probably intended to last all of the final season.

Any great arch should be written with the assumption of a full 5 year run with escape routes planned on a per season level.

Babylon 5 got the first part right and early enough in the fourth season found out it wasn't getting a 5th and wrapped everything up perfectly. Then, it got a fifth season which made the end feel very anti-climactic.

They should turn Misery into a series where rabid fans take over Fox and force all of their favorite shows back on the air.