Make it /qn if you really want it silent -- no user interface, for GPO or MSSCCM scripting.
Suggest that following a "silent" uninstall, you follow up with a run of the ESRI.APWR.ApRegWork.exe registry cleaner from the ApRegwork Utility folder on the ESRI_RiverHydraulics ftp site. At least a couple of times until until you know that the Microsoft installer is really cleaning everything related out of the Registry.
Let us know if it all works.
P.S. Below are the Installer Package IDs and Prduct Codes that I had available. I don't have installer packages for the earlier 1.3 and 1.4 products handy to check Product Codes against, but could probably dig them out if needed.