the thing about being ‘magneto’ is that you really, really need something that completely shakes your faith in anyone that isn’t an inhuman/mutant. jiaying has been around long enough to see WWII, in which the Chinese faced all sorts of horrible atrocities at the hands of the enemy. She may even be older than that. She may have been there for the Opium Wars. We don’t know. Couple that with the fact that she literally got dissected and you get a reason for her to have a complete distrust of non-Inhumans.
this post explains a lot about Mageneto’s world view. to quote it, “The evil he’s suffered is institutionalized. It’s not something done by individuals, it’s done on large scale by society as a whole, fostered by indifference, and orchestrated by the use of excessive control.” SHIELD may have a nice face on it, but to someone like jiaying or erik, it’s just another institution. there’s no reason for them to trust it.
so no, i don’t think skye could ever turn on SHIELD like that. i don’t think she’s had the suffering that jiaying and magneto have had. that’s not a bad thing! no one should have to suffer like that. but the fact that they did can’t be ignored. and the fact that people will suffer or continue to suffer also can’t be ignored. and for all it’s pretenses, i don’t think SHIELD can be trusted.