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In my application I need to drive a stepper motor and depending on the speed of stepper motor the device that generates the drive signal is selectable. Out1 is from rpi for very low speeds and Out2 is from an arduino. Only one of the output pin will be used in any instance. Will the following circuit protect the pin in output mode on rpi assuming the reverse voltage is around 700mV in the diode when arduino is driving the motor?

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    There is insufficient information about the "other circuit" to answer. – Milliways Oct 22 '13 at 6:42
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What you try to implement looks like OR gate and it should work as you write, providing the "other circuit" is well behaving, as stated by @Miliways (i.e. resistive load, grounded by reasonable resistor, see the wiki page.

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