Just reading over the opening post, I think you could make things a whole lot simpler and more in tune with Naoko's world if...

Small Lady ascended the throne shortly before NQS died of natural causes, either preceding or just after all of her senshi and Endymion die.
This would leave a well-adjusted team of four and the Queen to protect Earth, and you wouldn't have the Messier people so easily kill that many tried and true and tested senshi so easily. You could have them kill off the Quartet to show their strength, if you wanted.

When they attack and defeat/kill the Quartet, the Silver Crystal would surround Small Lady of its own accord, as had happened in the second arc when the black moon attacked. then you could either keep the Crystal Palace as the place where she sleeps enshrined as the sailor crystals of the solar system are naturally reborn and rise to defeat them and awaken her,

OR

Helios could use the last of his strength to hide her away somewhere in Earth or in Elysion, and fall into a deep slumber himself, receding to Elysion to await the day when he feels the crystals reformed yet again. He could rise as the person to fully awaken them, or serve as a guide once they find him.

The crystals would be naturally reborn on Earth as it is the only life-supporting planet in the Solar System and the entire Solar System would be under threat with these Messier people; they'd be reborn between 1000 and a couple thousand years later, but since all the solar senshi died at the same time, they'd be born at roughly the same time.

except the quartet, who would be born after since they died after (either in the fight our at the end of their natural lifetimes).

And so you'd have every crystal from the solar system up for play, with their predecessors having died of natural causes and so would have a new incarnation rather than a reincarnation.

I think I'll use some of both your ideas Kyra! Thanks!