Unless she has a danger sense that will warn her about tasteless sleeping pills, it should be possible to knock her out by mixing them with her food. Then pull out some nerve gas - I see sarin takes less than ten minutes to kill. And the best part? You can technically charge her while she's asleep.

Or... let's see. Methods for dealing with overpowered magical beings:

-Reality Room - negate her magic.
-Distraction - set fire to the forest or whatever, then stab her in the back while she's putting out the fires.
-Betrayal - pose as her friend, and use your position to implement one of the other methods.
-Chemical/biological agents, as discussed.
-A tripwire, and a large rock to hit her head on. Can she levitate? Can she do so in half a second?
-A bottomless pit. Though not if she can fly. Or teleport, I guess.
-Bury her twenty miles underground - head down. Even if she can blast her way out, she'll probably end up going deeper into the earth instead of out. Does she need to breathe? Though I suppose teleport might be her preferred option.
-Concentrated canon bombardment. Shove her into a television shop with the HP movies showing on every screen.
-Bring an agent who doesn't need to breathe, and get her to chase them through a portal to the ocean/space/wherever. Though again, teleportation might negate this.
-LSD. Dose her with hallucinogens and kill her while she thinks you're marzipan.
-GRR RAR USE TEH BIG WEPPONS TAHTS TEH ONLI WAI oh wait.
-Logic bomb. Meticulously point out all her logic holes (while not physically attacking her) and keep going until she implodes.
-Redemption. Befriend her, sit down with her, and calmly discuss the problem with Mary-Sues. Show her examples. Make her realise the problem, then get her to realise that her own nature is identical to what she's just condemned. Prepare to utterly horrify the Marquis de Sod.
-Redemption with a twist. Do all of the above, then when she vows to never use her magic again, say, "Good," and stab her in the throat.
-Guillotine. Disguise it, put something she wants in the basket, then activate when she leans across.

&c&c&c. To my mind, the best response to an uber-Sue is to find an utterly cheesy and silly way to kill her, not to try for similar levels of power. Think 'tear laura apart by geographical expansion', not 'kill Celebrian by suicide bombing'.

hS