You can uninstall the Web 2.0 and Mobile Toolkit using the Installation Manager command line.
imcl.exe uninstall com.ibm.websphere.W2MTK.v11 -installationDirectory installation_directory
./imcl uninstall com.ibm.websphere.W2MTK.v11 -installationDirectory installation_directory
Go to the IBM® Installation Manager Version 1.5 Information Center for more information.