If you check the “Show details” option at the top of the plugins menu it should allow you to select individual plugins to uninstall or deactivate. If this does not work as expected what version of NetBeans are you using? I check in my NetBeans 8.0.2 and NetBeans 8.2 and in both cases my JRebel plugin was listed as a separate plugin and not under the User Installed Plugins group.
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