Obito did deserve to die after all of the problems he caused. Even though he was manipulated by Madara at a young age at some point he became an adult and was responsible for his own actions. He could have walked away and not carried out Madara's plan. He liked the idea of the dream world and stuck with it.
Naruto's praising him, while weird to many people, is in keeping with Naruto's personality. Naruto operates on an emotional level and he did have the opportunity to see into Obito's heart when he was pulling the tailed beasts out. He saw who Obito had been before all of this and he also saw that Obito regretted his actions. Once Obito decided to help the alliance that was enough for Naruto. I would think he didn't forgive or excuse his actions as he didn't forgive Nagato. But Naruto would rather turn an enemy into an ally if he can in order to end the cycle of hatred.