I ran this past Atmel, who verified what you said. Programming a device so that the JTAG pins become I/O pins does indeed prevent the device from being reprogrammed via JTAG. As the ATF15xx-DK3 rig programs via the JTAG pins, not via high voltage, it can't be used to "unbrick" a CPLD.

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x86?  We ain't got no x86.  We don't NEED no stinking x86!

Thanks for the responses, guys. I did buy a new CPLD but at almost $14 each I'm hesitant to do much more experimenting. I also got a JTAG programmer which claims to be compatible with the Byteblaster mentioned in the ATF1508 datasheet.
http://www.ebay.com/itm/381197754943
However, if I start ATMISP with it plugged in, it gives nonsense error messages (which look like an amateur debugging attempt) and it just crashes. It did the same when I started the program just to generate an SVF file if I had my FTDI cable plugged in.

Do any of you know how to program it over JTAG without ATMISP?

I bought a ATDH1150USB-K ISP Cable. I'm running ATMISP,under Windos/XP in a virtual machine under MACOSX and never had any issues. This ISP cable is the only USB cable suported by ATMISP. The USB Blaster does not work.

cbscpe, check out page 13: http://www.atmel.com/ja/jp/images/doc1936.pdf

ByteBlasterMV and ByteBlaster refers to the parallel port ISP cables and not the USB Blaster or alikes.

I see what you mean. What I have seems to be a USB blaster. I can't get it working with UrJTAG or OpenOCD, though. I'm not sure what the problem is. This has been a pretty awful experience so far :/