I’m not sure adding an optional PvP flag to a full-time, PvP game is a good idea.
But aren’t you doing this wrong? Why not just put everyone in the non-wardeccable corp and the structures in the other corp with only a single alt (or even, individual corps each with a sigle alt)? The only thing then you lose is the ability to declare war, and to defend your structures in highsec, but gain the ease of logistics that everyone is in the same corp.
And, I mean that is kinda fair no? If you opt-out of the war system to be “safe” in highsec, why should you be able to defend a structure in highsec or choose which of your members is a combatant and which cannot be attacked by your war enemy? If you are a non-combatant corp, you are a non-combatant corp. And if you really, really want, you can always have the main corp ally the alt corp for defence, or have specific players hop corp. Or just don’t deploy a structure in highsec.
If you are going to be playing flagging games, expect some inconvience. If everyone could hide perfectly behind cover and only snipe when they were sure they would win, this would be a terribly boring game. The mechanics are suppose to put you at risk so you are not “safe” in exchange for increased rewards, and they barely do that with all the loopholes years of half-hearted “fixes” to the war mechanic have brought.