Perhaps the user has control over the disintegrating nature of the Truth Seeking Balls. Or alternatively, the user cannot concentrate on disintegrating nature whilst focusing on making and sustaining massive constructs? Besides, the TSB are made up of multiple natures and/or Kekkei Genkais. So I assume that the TSB can be made out of a base set of natures, and then other natures can be added, eg. Yin-Yang Release to nullify ninjutsu
Either way, the Truth Seeking Balls are a funky technique, and Kishi needs to explain just wtf is up with them, though he probably won't.
While on the staff sure. But off of it there is no reason it wouldn't heal her. It's not like the Edo Tensei where they are held together by ninjutsu.
Also keep in mind that Hiruzen was able to heal the damage done but Obito was in his crazy mode. This could imply that the Godama can only disintegrate something when the user wants to use them that way. This could be supported by Sasuke being able to stand on one, despite only ever channeling senjutsu through his left hand and Chidori.