In order to do this kind of hacking, the FPGA has to be removed from the target board and installed into a ZIF socket.

So this requires:
a) access to the target board (good luck with that)
b) the ability to remove an SMT device from a board without damaging it (good luck with that)
c) putting the part into a test jig with a ZIF socket (I suppose you could reball a BGA, but good luck with that)
d) and then what?

What's the intent? It's not like the hacker can remotely reprogram the FPGA to have to do some evil thing (like bring down a plane or focus a laser beam on the White House). The hacker needs to have access to the JTAG port in order to do anything malicious. Even if the hacker wanted to clone the device, he needs access to it.

Anyways, the flash-based Actel FPGAs aren't the highest-security options. If you want that, you're into OTP devices (other Actel families, QuickLogic, certain Xilinx and Altera parts).

-a