Jack may be an irrepressible 51st century type of guy but he is also a man that has lost a lot - his family, his friends, two years of memories stolen by the Time Agency.... He is also a man aware that not everyone is always on the up and up - recall the conman trying to dupe Time Agents with his quick clean up schemes. He traveled with the Doctor and Rose and discovered that it was more than possible to redeem one's self and to want to live as a good man, help those in need and all that. So yeah he was royally peeved at Ianto's betrayal with Lisa locked in the lower levels of Torchwood but he's well aware that people will do just about anything for those they love and that it still possible to come back from such a low. So Jack would value Ianto because Ianto has demonstrated his true inner self to Jack. Great stuff.