Alistair, as Warden, is the only one who calls bullcrap on the whole fake Calling thing. He ignores it. Perhaps "resist" is too strong a word. Granted, Stroud and Loghain do, too, but their responses re: if they hear when you speak to them about it are different.
As King, he also ignores it (if he hears it at all, discussion of that aspect on another thread).
The same song made Anders go literally mad when he got too close--so much so that Justice intervened and Hawke has to fight him to save him (in Legacy). Also, in Legacy, there are many notes that imply that Kirkwall's extreme blood mage/demon population is caused by the Prison being so close by--Cory's song affected them.
Perhaps, as a mage-blooded and elf-blooded, dragon-blooded Calenhad heir, he has a wee advantage. 
It's only theory. Thought I'd just add it to the speculation.
Re: dragon blood, what Rex said up there. Golden-haired son of Calenhad was just my euphemism for him, however, he's never referred to that way. 
Flemeth sent Morrigan with the Wardens so she could control the destination of Urthemiel's soul. That had nothing to do with Alistair either.
P'haps. If your Warden is female, however, it, of necessity, has everything to do with him.
Morrigan's extreme reaction to Alistair himself speak volumes, to me, but... again, implication. There's a lot of implication in Flemeth's stories, though--and this is all most of the theories are, born of implication.
ETA: [He's also Gaider's golden boy, so that in and of itself means he's some sort of Thrall character
]