I thought I already posted it.
0:30-1:00 and 6:20
Ganondorf's soul is removed from Zelda's body and the particles reform into his Ganon form. Ganon is killed and he comes back in his spirit form, where Midna attacks him.
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0:20
Then Hyrule Castle explodes and Ganondorf's back in the flesh, crushing the Fused Shadows.
At least 2 members of Team 2 can attack souls, maybe more (not sure if Bayonetta or War can, In my completion of Bay I cannot remember and I am not far enough in Darksiders to know of his powers).
Although War does absorb souls naturally,its gameplay just like how Dante can absorb souls but there may be some canon behind it, not sure.
1) It's a sound. You cant dodge sound; you can only block it.
2) Him being on Ganon's team is relevant to what, exactly?
The whole point was that Link has a degree of soul manipulation, meaning that he isn't a stranger to its effects.
Actually, Link is immune to those abilities anyway, via Master Sword and ToC.
Ganondorf has messed with his own soul several times. Aganhim was either a possessed body or a manifestation. Ganonondorf possessed Zelda and forced her to fight Link. Even Zant was given a fraction of Ganondorf's soul, which would revive both of them as long as the other was alive. How can we guarantee that anyone attempting to steal Ganondorf's soul won't be possessed? Or that he won't revive himself anyway?