Ziva went missing. Tony completely lost it. He couldn't lose her again. He couldn't go through another situation like last time. He was angry and irrational. He could have beat Kort to death if he hadn't backed off. Then when they finally found her, it was Ray she wanted. It was Ray who held her and Tony wasn't sure how to feel about that. Of course he was jealous, but he was also in a relationship. He shouldn't have felt jealous.
E.J. went missing. Tony didn't lose it. He was rational and calm. He could think straight. He was worried, but…there was a but. When he found her he felt relieved. But not the same relief he felt when they found Ziva.
He should have been more concerned about E.J. He was sleeping with her. They were in a serious relationship. But the fact still stands that he was more worried about Ziva and he has no damned idea what to do about it.