Reverse Polarity Protection: Is this method safe!
Yes, it's possible the surge could damage something (perhaps blow a fuse). The current could be quite high if the MOSFET is large and the source impedance low, perhaps hundreds of A, but not likely with only 1000uF. An ordinary 1000uF cap might have an ESR of a few ohms, so the surge would be maybe 10A for a few ms, no big deal most likely. Typically your load will bleed the voltage off quickly anyway. Bad layout might allow some transient negative voltage into your circuit, so don't do that.

Also, it is unlikely (but not impossible) that a user would reverse from a working to a non-working configuration. 

Never underestimate the ability of users to come up with innovative ways to break things.