If we must have such huge protection zones applied (ie, not just within the immediate vicinity of the spawn), then I think the best option is to apply them ONLY to new players entering the zone; not those already in it.
I would like to add that my criticisms are not just practical. Finding yourself suddenly caught behind enemy lines accounts for some of the most tense and exciting gameplay I've ever experienced. To remove that through forced "protection zones" which stop the player exploring is a shame.By all means, protect the spawns from enemy fire - but please find some way to do it that doesn't involve just turning huge areas of these otherwise beautifully designed battlefields into no-go areas.
Totally agree, I hate this form of spawn protection. Let the advancing troops mop up the stragglers if they choose to stay and the newly spawning defenders can take up new positions back near the new cap. Right now, once the attackers see the enemy turn tail and flee, they have a free pass to either sprint after them to gain easy ground or take target practice. It breaks the flow of the game, you go from intense battle to Benny Hill Music.