If the saw you there thing is what Elidibus says. That's not about what happens in the MSQ, but a hint to the 8 man raid post MSQ. Emet doesn't see the confluence right away. As he says it was never anywhere until where it is the instant he makes it visible. Heck they even tell you they're staying to help distract Hermes. Those two even somewhat agree with his dumb test. We don't know how fast Emet's horse is capable of traveling vs what little time anyone had left to escape. Meteion's sister were already traveling to their assigned planets by the time we arrived in Elpis. So we would have needed to jump back further in time to stop them from leaving the planet. They still would have wound up becoming the final boss of 6.0.

Stopping Hermes is akin to those alternative history fiction books that take a look at what might have happened if JFK hadn't gotten assassinated. Just because one good thing ends up happening doesn't mean everything else ends up all sunshine and rainbows.