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American Airlines has the BusinessExtrAA program, in which a business earns credit for its employees' travel in addition to frequent flyer miles the employee can still earn personally. It's not exactly designed for situations like yours, but it might help. I think other airlines have similar programs.

More information online at http://www.businessextraa.com. (If you key this in or write it down instead of copying or clicking, note the double "a" on the end.)