Disabling variable substitution inside SQLCMD script when using :r syntax
If you want to do the same thing that you are attempting to do within Management Studio, I think the simplest approach is to write a very simple PowerShell script to run the same thing that goes through each file and then executes the file with SQL CMD.  

In my example, I have a directory named e:\test. I have a few .sql files in that directory and I want to execute them and disable variable substitution.  To do that I would use the following script within powershell:

$Path = "e:\test"
$files = Get-ChildItem e:\test\*.sql
ForEach ($file in $files) { 
    Invoke-Sqlcmd -ServerInstance localhost -InputFile $file -DisableVariables
}


This obviously takes you out of Management Studio, but it should accomplish the task fairly easily and do so with variable substitution being disabled.