How safe is it to plug in an extension cord that has a missing ground pin in to a GFCI outlet?
Actually, it's not that dangerous at all.  If you're going to use an ungrounded extension cord (which is not recommended), plugging it into a GFCI receptacle mitigates much of the risk.

Having a grounding conductor in place, may prevent a fault condition from energizing grounded portions of a device (technically it won't prevent it, but it should trip the breaker). A GFCI should prevent you from being electrocuted, if you happen to come into contact with an energized portion of the circuit or device.

The proper thing to do, is to replace the extension cord.  However, if you're going to use the cord, plugging it into a GFCI makes it a bit safer (assuming the GFCI is in good working order).

WARNING: A GFCI may not prevent you from being shocked, but it should prevent you from being electrocuted.