I have exactly the same problem.
Need to update Adobe Reader on Terminal Servers without removing Adobe Acrobat 9.
Remove options are greyed out and 'Remove previous version of Acrobat' is checked.
I just tried it and created an .MST file and installed it to a Citrix server.
The Adobe Acrobat 9 has not been removed!
By default the installer for Reader will remove any previous versions of Reader. There is a command line switch (REMOVE_PREVIOUS=NO) which can be used to keep the old versions of Reader (which is not recommended by Adobe).
Reader installer will not touch the installation of Acrobat (any versions).
You do not need Customization Wizard if you only want to do this.
With Customization Wizard you can perform other customization like EULA accept, default PDF viewer, installation UI etc.