I would be more in favour of flags automatically going down if attacker is there for 2-3 seconds and no defender. Would make flag caps easier but would stop flagkilling. The invulnerability idea would mean flags uncappable, leaders with half a brain would get a few spawning every 5 seconds then all others to spawn at once then run round putting all flags up.
But I dont see what the problem is, so it fucks up your K/D who gives a shit? If you are that worried about it just dont spawn when flag killing is going on, I'm sure alot of the tryhards wont spawn into flagkilling already.