The company I work for (a $100M publishing co.) does the same thing. Since I work from a home office, I was able to negotiate the ability to book my own travel & keep the miles/points.

When I first started with this co., they didn't tell me the policy & booked me on flights & created new mileage accounts. What a nightmare!

I met with our Exec. Publisher & got him to agree to allow me to do my own bookings.