Disclaimer: I don't own Warehouse 13 and never will. No copyright infringement intended.
Pete didn't realize what he wanted until it was too late to do anything about it. Falling in love with Myka had been unexpected, and he was grateful she hadn't read too much into it. He wanted a family with her, but it wasn't going to happen.
Myka would never feel the same way about him, but he'd do whatever it took to make her happy. It was better if she was with some random person or HG, who he knew she was in love with. He wanted her to be happy.
Pete would stop hurting eventually, but not today.