Technically Sally isn't part of the Penders fiasco; Sega can use Sally anytime they want to, they just don't want to.
I've heard rumours that Ian Flynn would want her and the other FF's to return to the comics but admits they'd need a complete revamp to fit with the modern Sonic world. Sally, as she is now, doesn't have a niche in Sonic that isn't already filled by other characters, Blaze fills the princess niche, Amy for love interest, Jewel and Vector do various leadership and mission control roles, you get the idea.
Not to mention that she's only really known by western audiences, not Japanese, and is a pretty divisive character among said western audience anyway.

I've posted some art before that reimagines her as a squirrel and member of Blaze's royal guard that I feel could work.