While an exact timeframe wasn't given, the book seemed to indicate that the affair lasted for a while, maybe a few months - long enough for them to develop a real relationship. After her death, Pine admitted to himself that he had loved her.

Yes, clearly he was willing to help her before they were involved because he knew it was the right thing. He had been a soldier in Iraq.
But does anyone really know how long they were involved? It could've been 2 weeks or 2 months for all I could tell.
Ultimately it made more sense to me than he and Jed, which seemed to come out of the blue and was extremely risky.

He also got involved because of the damage the weapons were doing, which he saw 1st hand during his tours in Iraq. His chef buddy even asks him if it was about Sophie and Pine says Yes and No.