They wouldn't be able to reboot at 0% - their options would be rebuy or stay and wait. Remember their ship is disabled, options that are available at 1% or greater would not be available. Technically they are dead with a chance at being res'd by a third party.
Yeah and they can combat log, self-destruct, reboot... This would be a totally different scenario.
As a developer I'd say its very possible to change a defunct, no longer owned player ship into an NPC ship for the remainder of an instance. You don't need PES for this because you do not need it to remain there permanently, only until all players have left the area.
See my first response, this is not the same scenario as thrusters disabled, ship functionality will be disabled (except reserve life support). And I've already stated what the advantages are to this beyond ship boarding several times.