Usual disclaimer applies.
This is set prior to episode 5x16, when Lorelei is captured by Red John.
There can be no victor now, Red John knows.
Patrick Jane, the man he brought low in retribution, proved his value and chose life. Justifying his mentor's decision to spare him and take his family, his distractions, instead.
He'd watched Patrick from afar, before the TV debacle, and wished to collect him and his skills set - a valuable addition to the 'confederacy'.
But Patrick proved resistant to enlightenment. In rejecting the higher path though, he became something exciting. A worthy adversary.
Destroying Lisbon would destroy Jane. But that would be game over and that would never do.