Fire flowers, yes, but why use a gun when you can throw a Koopa shell at someone? Guaranteed hilarious. And how about hammers a la Hammer Bros.? Or feeding a Sue to a pipe-plant? Chucking her under a Thwomp? Lava is always good, but not very original.

I'm not really familiar with anything after Super Mario World (which was totally awesome), so I might be missing things, but my point is that there's a lot of room to be creative in Mario, and being creative is always a good choice.

Whatever you do, you probably have to be sure the Sue is out of lives before leaving.

~Neshomeh

You'll have to "hack" the world in which the fic takes place to do it, but thankfully, there's a way for agents to do it: Describe the badly-described scenery to re-form it the way you want.
http://ppc.wikia.com/wiki/Poor_description

This isn't altogether safe, because all of the laws of irony tend to apply; but it can be done and has been used (though I'm not sure it's been used as an execution method). Canon tends to help you because it wants to be rid of the sue/stu as much as you want to kill them.

Ever had a lucid dream? I think it must be a lot like that. You know you're dreaming; so you can create things and events just by expecting they'll be there and imagining them vividly enough. Only sometimes, it doesn't work well; or you can't keep the details in your mind; or you can't control things entirely because your attention wanders or you're subconsciously expecting something else to happen. (If you've not had a lucid dream, or not learned how to control them, chances are you sleep too deeply, you lucky bum, and don't get woken up every time the air conditioning switches on...)

Set aside some Bleeprin for your poor agents, Sneezier. They're going to need it.