A quick explanation:
Fortresses are unique, but sites are not, so even though there are 2 "Herod's Temples" in play there are not 2 unique cards with the name "Herod's Temple" in play.
The reason the protection doesn't end is because protection is an ongoing ability, which last until the end of the phase when not specified, so even though Isaiah's ability goes away (in the sense that the card no longer has it (see converted heroes losing abilities) and is no longer in battle) the ability lasts until the end of the phase.