Doubtful you can get an FPGA of that class in a thru-hole package. The dude was smart to shop out the PCB instead of spending weeks trying screen and drill his own.
You probably can get FPGA in CPGA package that has similar performance to that Spartan3, but these things are meant for high reliability and wide temperature range military/aerospace applications (you get either THT or really funky SMT packages there) and certainly beyond the budget of most hardware companies, not to say any hobbyist.
Not like it's really that hard to solder SMD. I soldered 40-pin SMD all the time with nothing more than a fine-tip soldering iron, a syringe full of flux, and a magnifier or microscope.
Speed of the FPGA? FPGAs are given speed grades, but the actual design dictates the max speed. Different logic sections, depending on pipelining, size, which pins they are connected to can run at different speeds. You might have an overall max speed/critical path of say 50mhz, but you might be able to safely run a small section of the design at 200mhz.