I actually feel kind of sorry for Jacob.
Zoey's story demands that one of the DIKs has a thing for her and has to check if MC is cool with it. Zoey then has to confront MC being over her or not being over her. Either way she can't ignore what she feels herself. Jacob is sacrificed for that role. It's very natural that he would be attracted to her. They share interests and Zoey's behaviour being misinterpreted as flirting is established in the interlude. He gets a crush on a girl who isn't interested. Poor guy.
I really want to choose the option that is easiest on Jacob on any run that is indifferent to Zoey, but I'm not really sure which one it is. Giving him permission seems like the right one, but it might be easier for him to think that he deserves to be shot down for being a bad bro.
Of course if Zoey's confrontation with the chosen main girl is particularly juicy I'm going for whatever option makes it best.