Either I have not been reading the Synapse announcements closely enough (likely) or I don't understand "since we will have maybe other uses for stamina..."
Does this mean that when the new system comes out, we might be able to use Stamina for something other than PvP Faction Wars? If so, then factions that use WB to win wars will be hit even harder. First, they won't be able to use WB for refills. Second, if Stamina is useful for things other than Faction Wars, then players will be tempted to (or need to) use Stamina outside of Faction Wars. Both of those things would reduce the total damage a WB-using faction could inflict.
Of course, any reductions might be offset by other changes, so my speculations are merely speculations.
Fortune favors the well prepared, however, and a faction that wins with War Bonds would be wise to prepare now for the possibility that a faction war system without War Bonds will significantly hurt the faction's strength in Faction Wars.