Pagan Min never wanted to kill Ajay Ghale. He's always nice to you, regardless what you do. Whether you killed his double, liberated all outposts and fortresses for the Golden Path, take over all radio towers so Rabi Ray Rana broadcasts all over Kyrat, killing most of the Royal Army and Guards, kidnapped Paul De Pleur Harmon, killed Yuma, destroyed his golden statue, he is always on your side no matter what. Even in the beginning of the game, he killed one of his Royal Guards because that guard specifically ordered other troops to shoot the bus, pointing towards Ajay Ghale. Ajay Ghale almost died, and Pagan does not care about any human being that will endanger Ajay Ghale. AJay Ghale was following his father's footsteps who was leader of the Golden Path, thus he helped the Golden Path win the war. Pagan Min hates Ajay's father, Mohan Ghale, for killing Pagan's one year old daughter. Since Mohan is the leader of the Golden Path, Pagan considers all those involved of the Golden Path, except Ajay Ghale, as terrorists. He also brought Dharpan, "Ajay's plus one", to dinner. However, Dharpan had to text to Sabal, who is part of the Golden Path. Pagan found out that Dharpan is associated with the Golden Path "terrorists", therefore he ordered Paul De Pleur Harmon to interrogate and torture Dharpan. De Pleur calls himself as a good guy, because he believes he's fighting for the good fight. If Dharpan did not text for help to someone who is likely one of the leaders of the Golden Path, he would've enjoyed his stay. He wouldn't be tortured at all.
When Pagan meets Ajay in prison, he considered it as "tough love", or "prison love". He would rather contain Ajay and let him live than let him live and kill more people, but Ajay escaped anyways. All those that tried shooting and killing Ajay, Pagan doesn't care about their lives. Even if it's his entire military trying kill Ajay, Pagan still wants Ajay to live no matter what. Golden Path are terrorists, and anyone supporting them, are considered as bad guys in Pagan Min's eyes... except Ajay Ghale, who happened to be his stepson.