The short question is: what can she away with?
Now here's the long version. A Runelord successfully out of hibernation is going to want to save time with the rebuilding of her capital city, much less her empire. Picking apart the wish according to the criteria of what's ideal (Legacy of Fire: the Final Wish, p.58):
? Trusting the genie not to screw you over: Twist the wish or offer a lesser service? Whatever least antagonizes the gal aiming a maximized polar ray at you, that's what.
√ A clear and concise wish: "Restore my empire to its previous glory."
x Keeping reality-warping to a minimum: The Runelord's asking for a huge geological and complex architectural reworking which was initially caused by an antagonistic third party.
Wishes a far too random (especially when granted by a third party that may or may have your best interests at heart). Runelords can live forever and are therefore more likely to implement long term reclaimation efforts such as: Animating a horde of undead/construct servants. Conjuring/binding some extraplanar help. Enchanting/dominating the local populace into a work-crew (or threatening to set fire to them if they don't do what you say!)
A potentially random effect, like Wish, could undo much of their "Good" work.
Spoiler warning, but there's precedent of a runelord using wish spells for far more minor things. I agree with Mirrel, risking the unintended side effects is probably not worth it.