Near the end of movie Muska was holding Sheeta prisoner while slaughtering the army using the power of the crystal.
Was there a reason why he was letting her live? Did he plan on killing her afterwards or using her as backup somehow.
Maybe he thought she'd know more secrets about Laputa.
You are sin.
Like Muska, Sheeta was also a descendant of Laputa. I don't know what Muska's exact motives were but keeping a person with the same descendancy alive even though they had conflicting ideals makes a lot of sense to me, assuming not many of them or none other still exist.
Some of the options could be convincing her to rebuild Laputa to its glory together, enslaving her or marrying her (making her his queen?) in time. Muska seemed to want to own Laputa and rule the world through it, and probably thought Sheeta would be a useful tool in the process.