I think Idea 2 is possible with the right amount of control. People need to understand that losing a war or fight isn't always a bad thing as far as RP is concerned. Say Planetform got found out that their entire theory on terraforming got found out to be a hoax. They either dissolve, or go underground, maybe even hold Harris, Ayr Atka for randsom. An underground faction always makes flying for them more interesting. Seeing a faction like the IMG obliterated where they stand and pushed into the hands of other factions or changing their faction's nature completely is just, cool.
Any faction that loses a war can easily be turned into a faction as hard and sinister to find as the order was in vanilla.
Both factions need to agree what happens to their bases and systems outside of the RP environment in order for the new changes to occur. If they keep bitching for a longer than normal period of time then simply nothing happens.