I am currently automating our iOS testing on jenkins. So far I had no problems with running unit tests, converting OCUnit into JUnit and generating code coverage in Cobertura fo
From my understanding code coverage files get generated when the app quits, but you can't just kill the simulator.
Have you tried creating a separate target for your app where you have the info.plist property "UIApplicationExitsOnSuspend" set to true?
There is a slightly wider problem, however. The generated coverage files aren't cumulative and get overwritten each time the application quits. So, depending on how your tests are structured (i.e. are you killing and starting the app for each distinct test) then you may struggle to get decent code coverage.