The wookies are not extinct, Kashyyyk was enslaved by the Empire for years. In the Heir to the Empire trilogy Leia goes to Kashyyyk to seek protection with the wookies, and there are plenty of wookies still around. Also in Star Wars Galaxies Kashyyyk and the wookies are alive and well, tons of wookies running around in that game Jedi too now, but that's another debate entirely
Also in the original X-Wing game, on one mission you had to rescue some enslaved wookies on an Imperial freighter. The movies only give you a small glimps of the universe, the rest is left to you to fill in the gaps. I don't think Lucas ever had the intentions of making the Wookies extinct.