I finally got around to this part of the game after a logged 4 days solid worth of gameplay, and now feel as though I can comment fully upon the topic material.
After speaking with Father (Shaun) I can give my thoughts on certain key parts of the conversation. First, yeah... he was a bit of a dick with that rotten trick of making you think the kid was him. However, I do add some points because of his raw honesty with being upfront to you about him, his life, the things he's done... You gotta admire him for not trying to hide some of that evil s***.
Now, the part where he calls your spouse "collateral damage," a lot of you guys seem to be taking that out of context. I don't think he's actually calling your spouse that, so much as spitefully paraphrasing the reports he read, regarding how his prior superior had worded the brutal murder. In fact, he later went on to honestly admit that letting you murder Kellogg was some very satisfying revenge. Some of you guys say this makes him a sociopath, but I tend to view it as him being more vindictive for the alternate life he could have lived had Kellogg not kidnapped him and murdered one of his parents.
Afterwards, should you say you pity Kellogg, he expresses surprise, because here is a parent who went through hell to find him, and forgiveness for the man directly responsible for everything is... very out of character, given all the things you've done up until this point. I view that as justifiable surprise all things considered.
For me, it seems like Shaun now finds himself with a bit of a moral conflict. On one hand he has his entire Institute oriented life which has trained him to think only in terms of logic, rules, and cold scientific thought. Then on the other hand he suddenly finds himself with a loving parent he has never known and struggles to comprehend. In short, he's torn between being cold and emotionless The Administrator, or discovering his past buried emotions to a parental figure who refuses to reject him.
This seems best represented in your last interaction with him right before he dies. Indeed, I admit that this makes him a very tragic figure...