The problem is, let's say the WoL gets some major vision of things to come, which causes them to be completely at odds with the Scions. Given the relationship between the WoL, the Scions and even Cid's Ironworks, I think it would just boil down to the scions (probably Y'shtola) demanding an explanation. Once talked out, they'd trust the WoL and follow the hero's lead.

I mean, unless we're talking something like mass genocide which...really..who wants to play that game and be that kind of "hero". Would never happen.

The only thing I can see would be something like after destroying the Ascians and ultimately Zodiark, we then have to take out Hydaelyn. Or the 12 gods (who I'm pretty sure are just Allagan ancients or Ascians anyway). Even then I'm sure they'd just follow us to the ends of the earth.