The Uninstall thread in SO is correct. You can uninstall your Hibernate plugins by going Help -> About IBM Rational Application Developer -> Installation details. On the "Installed software" tab click on the software that you wish to uninstall, then click the "Uninstall..." button.
Adding as an answer.
I presume you used p2 to install Hibernate (Help > Install new software or Eclipse Marketplace). P2 has a command-line utility to run headless installation processes. In this blog post, I depict how to install RTC on top of RAD https://www.ibm.com/developerworks/community/blogs/victorsh/entry/installing_rtc_client_402_on_rad_v90_in_command_line?lang=en What you need to do? Find out the feature group for Hibernate and use the uninstallIU argument http://help.eclipse.org/juno/index.jsp?topic=%2Forg.eclipse.platform.doc.isv%2Fguide%2Fp2_director.html
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