Does the same thing happen if you use the electric starter to re-start the engine?
My Subaru's ECU is much better-behaved now that I've installed an engine kill switch instead of cycling the ignition. It idles very high for the first few minutes after you turn the key to ON. Maybe Toyota's ECU is doing something stupid, too. Try killing the engine by pulling a fuse, then push-starting, and see if it misbehaves then, too. If not, build a kill switch.
But yeah, low idle could be injurious to your engine.
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