You're using Mara Jade as a character. You've already deviated from canon. Do what makes you happy.
Mara Jade no longer exists!
Would this be unethical?
Mara Jade no longer exists!
She escaped the destruction of the EU by hiding in an Infinite Backpack!
Mara Jade no longer exists!
She escaped the destruction of the EU by hiding in an Infinite Backpack!
Infinite Backpacks are a mechanical min/max of the system. It will have to vary based upon local GM rulings whether they are allowed or not. 
If the Infinite Backpack exists then Mara escapes destruction. If they don't then she is erased from canon with nary a cry from her and will be forever remembered as Sneake's loyal wife.
Edited by ThePatriotpssh, I wouldn't concern yourself with what's canon or not. Characters are being made up anyway...in this case, just "make up" a character named Mara Jade who is an Emperor's Hand, for all the good canon means in RPGs 