Yup, Thunder is the Marvel who's appeared in the current incarnation of the Legion. I didn't mind Thunder all that much (unlike many other readers), probably because she WAS a member of the Marvel family. But it appears that TPTB don't have any plans to have her return anytime in the near future, either because they want to focus on other characters, because they don't want a surplus of "Kryptonian-level" powers around (i.e., M'Onel, Andromeda, Ultra Boy and Star Boy at times), or possibly both.
In theory, though, it would be cool to have CMJr. as a Legionnaire.