1. It was always his intention on killing Kate but he needed the rest of the team to feel worse then they would if she just died. Gibbs would think it was his fault and be consummed by guilt, Tony was in direct range of the 'splatter' and would feel sick to his stomach because his face was covered in his now dead friends blood, but what about McGee who wasnt on the roof? I believe that Ari shot at McGee and missed him on purpose so he would think that he was the first target and suffer from survivers guilt.
2. It didn't acctually matter which Agent it was. He must have done some research on the team before hand and he must have known that nothing ticked Gibbs off more than his Agents being in danger. I believe that Ari knew about his fathers plans for himself and Ziva and wanted to get her out of that world so she wouldnt share a fate with their younger sister, Tali. Ari killed an agent to create a vacancy on the team that would hopefully be filled by Ziva. He wanted ZIva to experiance the care that Gibbs has for his agent, therefore giving her the father that wouldnt end up destroying or killing her like Eli had done to Ari and Tali. In the end it was just an older brother looking out for his little sister.