The Strawberry Mountain Wilderness just south of John Day is another possibility. Be sure to allow time in your travels to/from to visit the John Day/Fossil Beds National Monument, especially the Painted Hills! Another possibility is the Elkhorn Range just across the Powder River Valley/I-84 from the Wallowas. The Ochocos and Blues aren't as spectacular but have some wilderness areas with pretty hiking (Mill Creek, Canyon Creek, N Fork John Day, Wenaha-Tucannon, the last mostly in SE Washington). Or Steens Mountain. The later in September you go, the more apt you are to run into snow issues at higher altitudes. Last year (I believe) they closed the Steens Mountain loop in late September and had to haul out some snowed-in vehicles. That's unusually early, but it does happen. Steens may be in the desert, but the summit is almost as high as Mt. Hood. It's probably too far for what you've planned, anyway.
Check conditions first with the local ranger districts. (For Steens Mt., the BLM office in Burns.) Also the weather. It's supposed to rain in Oregon, this weekend, too!
There have been plenty of severe thunderstorms/flash floods in Central and Eastern Oregon this year. All over, in fact--this seems to be the year for them! In the Wallowas in September, if it storms it will probably snow (it will melt off), and clear nights will be below freezing. It can be beautiful, though, and the crowds are gone.
Also, keep an eye out for hunting seasons. In some places, special permit seasons start in mid-September. A blaze orange vest that covers your pack might not be a bad idea. General deer season starts in early October and is best avoided altogether.
You might want to check Portlandhikers.org (both forum and field guide) for info on the Three Sisters Wilderness.