Cannot commit configuration changes because the file has changed on disk
There are many different things that can lock the applicationHost.config file and cause powershell commands like New-IISSite to fail.
In this case, you mentioned you deleted the site manually so perhaps you still have IIS Manager open and it is locking the file. I suggest closing IIS Manager.
As described in this blog post on Powershell and IIS, the makers of Octopus Deploy have found that the only reliable solution to the file-locking problem is to wrap any file-altering commands like New-WebAppPool in try-catch blocks and retry these operations multiple times. The source code for a function to do this is found in the blog.
It seems something really screwy is going on with New-IISSite command. I ended up dropping back to New-Website (via WebAdmistration module), and all the problems went away.