It may be the case that a plugin requires an specific environment or may whack/replace some existing artifacts. It would be a good idea to let the developer know and make a choice of continue with the installation or stop it.
I believe a workaround would be to place a check on scripts/_Install.groovy, possibly calling uninstall if the developer does not agree with the plugin's intentions. The problem I see with this is that it may be too late, specially if the plugin has dependencies on other plugins that are not installed (they will be pulled too).
- check for JDK6/JDK7 before installing
- slideware plugin replaces Application.groovy altogether
- swt plugin may replace some config files