Any suggestions on how to resolve a secret identity with the String mechanic?
Yeah. I'd resolve it as such: When you have Strings over someone, you have power over them. It doesn't matter whether you're in disguise or they're in disguise.
If the Chosen says "Stop!" and chases after a werewolf, they can still yank on that emotional control they have, even if they don't recognize the werewolf. The fictional input here is "The Chosen yells stop and gives chase," and the mechanical input here is "The Chosen spends a String on The Werewolf." It doesn't matter if the character knows what the String is, so long as there's both mechanical & fictional input.
Picture this is Buffy. Buffy yells "Stop!" to a Werewolf, not realizing its Oz. The camera cuts to Werewolf Oz's face, which contorts in a fit of confused panic. The humanity of his character is coming through, even though he's still wolfen. Buffy is getting the advantage of her emotional power over Oz, even though she doesn't realize it. (But her player definitely realizes it, if we're talking about an RPG sitch!)
As long as you follow the "when you do it, do it" principle, then a person can spend a String on another regardless of any weird identity swapping or disguising or whatnot.