I have a few guesses, and you may think me crazy for mentioning them, but just try to keep an open mind. And like I feel free to disprove any theories. If you make a good argument, I will update this and put it in as a later chapter. 

Guess 1: Gethen

Okay, okay, I know I'm crazy. Just hear me out ok? The Black Swan didn't know who was in the neverseen when they made Sophie. Also, Gethen has blonde hair and is a telepath. I know, Sophie might have gotten blonde hair from Oralie, but you have to admit it is possible. You may argue that Mr. Forkle knew she was going to have telepathy as an ability, so he obviously put it in there like the polyglot and inflictor ability, but we also know enhancing and empathy are connected, and Mr. Forkle knew she had enhancing as an ability.  He could have just studied her genes and tweaked them.

Guess 2: Fintan Pyren

My first argument is the same as Gethen's. The Black Swan didn't know who the Neverseen was at that point, and they let a Councilor donate DNA, so why not let a random person who wants to donate DNA donate it? Also, how would the Neverseen know about Sophie, to come and to try to grab her before Fitz did? I mean it is true that Alvar is in the Neverseen and went looking for Sophie for a while, but he passed over Sophie as soon as he saw her, thanks to her extraordinary eyes. How would Gethen know to come to grab her if Alvar passed over her without getting a better look?

Guess 3: A Character we Haven't Met

Other than these there aren't many logical options. Alden and Quinlin wouldn't have done the break on prentice if they were her father, Grady didn't trust that Black Swan after he thought they killed Jolie, Mr. Forkle is two people so they couldn't both be her father, and I can name a lot more reasons why other people aren't her father, but I will stop talking and let you keep reading.