The virus ICE-9 has a file name extension of 'exe' which is a Windows OS only executable extension. When Finch breaks in to NSA data-center to upload the virus, it says on screen that he is uploading ICE-9.exe to all NSA servers. It is however, next to impossible in a data-center that all servers run on Windows OS. Servers running on Unix OS are definitely present. So the ICE-9.exe virus would have no effect on servers running on Unix OS and thus Samaritan would not be affected completely by this virus.
They provide alternative scenarios of what would happen if Finch never invented the machine but in Shaw's alternative storyline she's working for the machine as a government assassin. From the conversation with the target it's clear that some type of machine is in operation, and even if there wasn't, the government would have assassins with or without the machine's input.
Finch takes a self-driving Tesla to the airport. At the time this story was taking place, Tesla didn't have a full self driving ability and its self-driving capability was very limited in its abilities.
Uploading the ICE-9 virus will not only kill Samaritan but also The Machine. This, however, does not make any sense as Finch knows about the virus so he could easily have added a patch file against it to the Machine. That way the Machine would be protected against the virus.
Shaw was in the Marines, so she would know that she is not permitted to wear her hair down in uniform; putting her ponytail inside her shirt is preferable to allowing it to fall below the bottom of her collar.