Isn't it funny how you write a minor character, but even that small part of your writing reaches out to someone? The post-Disneyland conversation where Jake gets all choked up really touched me.
Anyway, deserting his wife and son was certainly not defensible. He was weak and selfish, and he really hurt them. At the same time, I think you really showed in the last 2 chapters how his actions are understandable, and, one can hope, eventually forgiveable.
Understandable in that for almost 2 years, he was starved for affection; his wife couldn't accept comfort from him, and in her depression froze him out sexually. And after she slowly recovered, the dysfunctional pattern of interaction established over the long bad stretch had become habitual, and couldn't just vanish instantly. Even while still loving his wife & son (and from that post-Disney phone call it's clear that he never stopped loving them), I can empathize with how he would still be dying a little every day, and it just wasn't enough.
Forgiveable because, just as you said, he's only human, full of weaknesses and frailties. Just struggling to be happy, like all the rest of us. Then he fell in love with someone he shouldn't have fallen in love with, which again I can totally empathize with; I think all gay people understand at least a little about not being able to help who you love.
Plus, I think it would be a real coming of age and step of maturation for Perry to come to see his dad as human, learn to forgive him and love him despite his weaknesses, and also come to stop prejudging Jake's new wife as "that b**ch" who stole my dad away. It would be so healing for both Perry and his dad. Perry has a big heart, and I think he can do it.
So I guess you could say that I'm a Jake fan in that I'm rooting for him (& for Perry).