SQL Server Client configuration via file
The data about connection aliases is stored in the Registry, so either a .reg file or a script that updates registry would do. Updating the Registry can be done with reg.exe or Powershell.

The tricky parts are cliconfg syntax and the fact that 32/64 bit registry keys are not the same. That is, 

HKLM\SOFTWARE\Microsoft\MSSQLServer\Client
HKLM\SOFTWARE\WOW6432Node\Microsoft\MSSQLServer\Client


Take a look at this article about 32/64 bit versions.