WotC is actually pretty cool about allowing its staff members to do freelance game design. We must ask permission before taking on any projects, but said permission is almost uniformly granted. A careful look at the credits of many d20 products will reveal several Wizards staffers working on products.
Heck, Chris Pramas owned Green Ronin while an employee here, and Darrin Drader (Dark Portal Games) works at the company, as well. I've contributed to four d20 products, editor Jennifer Clarke-Wilkes has edited several books from Green Ronin, and I can't swing a dead hellcat up here in periodicals without hitting someone who's using his spare time to cobble together some d20 project. Bruce Cordell is on his second (?) product for Malhavoc Press.
Most of us also do freelance for Wizards of the Coast, of course (which explains why my name is on the cover of Faiths & Pantheons).
--Erik