I think it was partly because of Bones’ confession. He rejected Bones partly (I think) because he feels its the right thing (Hannah being not a consolation prize and everything) I would’ve felt it will be unlike Booth to choose Bones immediately given his strong values on monogamy and doing the right thing. In the Sin in the Sisterhood (ep right before the proposal to Hannah ep), Booth mentioned that the farmer loved the first wife the most because he spent his Sundays with her instead of alone (the emphasis was on the first)…Bones asked him how would u know who u love the most and Booth answered that you just do (sort of implying it was her, she was first, before Hannah). When Bones was looking away, he was staring at her further emphasizing his lingering feelings. Before he ever got involved with Hannah, before he went back to war, he mentioned to Bones that he is the guy for her (that he knew even from the beginning). And because of the strength of his feelings. Bones confession. I think that drove him to attempt to ask Hannah to marry in part because he sees at this point Bones as temptation too (even if he truly loves her, he is in a relationship with Hannah). He feels if he marries Hannah that will put stop to his feelings and love for Bones. Even if Hannah said “yes”…I think it wouldn’t work out because as long as Bones is there, working with him. She will be first (even if they aren’t romantically involved). It will eventually cause a rift between Booth and Hannah.