I use Yamaha's DTX400K, which is pretty similar to the Alesis. The Yamaha only has USB for MIDI (no 5-pin DIN). I installed the Windows drivers, plugged in the kit, fired up Reaper, and activated the DTX as a MIDI device for input. It works fine for me. I use it to drive SSD4, EZDrummer, and recently I got Superior Drummer as well. I haven't done much SD yet, but I did at least test it out and it worked without issues.
I think the main benefit to using a MIDI input instead of USB is that you're not limited to such a short cable. That'll afford you some freedom of where you can put the kit in your room. I have to keep mine very close to the computer because USB cables don't get much longer than 10-15 feet.