I'm going to be trying this solution from a much older version:
I. Silent (non-interactive) Installation
NOTE: This procedure requires Administrator privileges.
The MATLAB Compiler 4.4 (R2006a) MCRInstaller.exe has a silent option. To perform a silent install to the default location:
MCRInstaller.exe /w /s /v/qn
This command uses the following flags:
/w is to wait for exit
/s is for silent
/v passes qn or query number to MSI installer
NOTE: Spacing is important in this command. There must be spaces between each of the flags, except between /v and /qn.