I always say "honesty is the best policy."
IN my company, our travel rules state "Anything that is booked for the the company is the property of the company. that includes air tickets, hotels and other stuff."
The good thing is that our travel department does not want to be "bothered" with Frequent Flyer and Frequent Guest programs. I think there are five people in my whole company who belong to FF programs so we get to keep the miles.
I would talk to your company and see if any reinbursement is possible. But never try to pull any tricks...they come back to haunt you eventually.