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I really thought it was no big deal and it was only a few things here and there. But I've removed near dozen tables and hundreds of options (many of which were on autoload). There should be an option to delete a plugin completely, I think that should be the default.
This is why I no longer install stuff willy nilly in production environments. I try them out in a dev environment before adding them to production. I exclusively seek out plugins have a reputation of being “clean”, lightweight, and non-instrusive. I also try to use custom code snippets where I can, though of course I can’t write every functionality of every plugin.