It's always been unclear to me what the role of a sage is supposed to mean. Looking at all games, it doesn't look like they disappear from the physical world. Medli and Makar for example, they both awakened as sages before joining Link to the temples, but they never lost their physical forms. Now one could argue the sages had died in Ocarina of Time, but that would give a question mark on Wind Waker why they needed to awaken new sages if dead sages would do just fine. At the end of Ocarina of Time, they all stand together on top of Death Mountain, indicating they are not bound to their temples or some spiritual realm at all. So I doubt the sages would never return to where they came from. It seems they're just people that have an awakened status, and have been guarding the temples until evil has been defeated. So in the end when evil is defeated in OOT, they wouldn't necessarily need to keep on guarding the temples and thus should be able to return.
Also, I've been looking up that Gossip Stone quote, but all it refers to is Link and not Kokiri in general:
"They say that one Kokiri has left the forest, but he is still alive!"