Yeah, it'll work fine. Too many folks get all worked up and think if you change the exhaust in any way with no tune you'll damage the engine or the bike will run terrible, not so. Having the bike tuned is ideal and will make it perform at it's best, but isn't a must. There's a thread here where a member used the stock gen1 header and one of the stock mufflers for a cheap single side system, and he says it runs great, no suprise.
The performance may/may not be what you hoped for, but again, even that exhaust can be tuned to run better. Check out Boostbysmith.com(site sponsor) for the ECU Editor. It does alot more than a power commander.