Change site name

On my end(Europe) it is called Main Site, but for you it might be called "Company"
It is not possible to rename the "Main Site".

What you need to do is to actually ignore "Main Site" and leave it as a place holder. For example if you currently have 4 sites + 1 Main Site, then ignore the Main Site and create a 6th site and name it however you like. Reassign all users, call queues & IVRs to the 6th site.