1. Yes, you really shouldnt be flipping zones solo. But sometimes a job just has to be done. And Being SF to flip zone has nothing to do with PvP. You generate factional presence (from here dorth shall be reffered to as FP) just by being SF which in turn helps flip zones fasters. And though I cannot argue this in good faith due to lack of testing, but generating GCW points while SF increases the amount of factional presence and flips the zone faster. Combatants being able to immediately flag up does nothing but make zone flipping harder than it already can be as the moment they flag, their FP will overtake yours simply by presence alone. Factor in the previously stated set up with potential to insta-incap, and the attackers would easily undo all your progress due to increased FP from the player kill and the GCW also generated from it; potentially erasing all the progress made.
2. I wasnt using Vreni Island as a scenario. I was using it to prove the point that sometimes it is necessary to be SF and solo in order to take control of a region. But even in the scenario you suggest, you neglect to tale into account that Vreni Island is an ISLAND. Once the attackers gank whoever is SF, they can leisurely mount their speeders, begin flagging down, and just stay over the water where they cant be attacked by any means.
3. If your suggestion of combatants being able to attack SF players were implemented, i can GURANTEE you would have groups of combatants roaming looking for SF players. Even if the SF defender were fully geared, a group of combatants could most likely take them down by the element of surprise and numbers alone.
4. Whether or not it is fitting for a "war scenario," you still have to balance the game like a game. SF already appear on the world map with a moving waypoint to every player regardless of faction affiliation or combat status from the GCW Factional Presence tab. Neutral entertainers in Mos Eisley can see exactly where SF players across Tatooine.
5. This is all failling to take into account the consequences that come with the ability for combatants to attack SF players. There would be no incentive to flag SF for PvP when being combatant grants you the ability to get a surprise attack that can immediately put a SF player at disadvantage. This is also failing to account for the change to officer rabks coming int he Phase 2.0 GCW update where it has been stated that Officers would pernanently by flagged for SF, exasterbating all the other issies brought up in this thread