The view from Harry Kim's apartment would be impossible. Its established multiple times in the episode that Harry lives in the Mission District but we can clearly see the Transamerica pyramid and SF bay from his window. The only way this angle and height would be possible would be from Nob Hill or possibly Chinatown. The Mission District is simply too far away and south to get a view like that.
"Cosimo" could have gone to Starfleet headquarters with Harry to explain the situation to the Admiral. They would've taken the anklet off and allowed Harry to work on how he could've gotten back instead of breaking into the runabout and having the firefight in space with Tom Paris being killed. (If the method of returning to his reality didn't work.)
The entire time Ensign Kim is running away from security, he has his communicator badge on and a security anklet. They should be able to lock on to either and beam him into a prison cell.
In addition, there would be no need for security forces to respond at all. Simply add a program that call for beam out to a secure location as soon as the anklet is tampered with.