There are two ways around this problem...unethical and ethical.

The unethical option is the one most often practiced - wait until the sub-100% fares are gone, then go to the travel portal and book the ticket.

The other option which works best at a smaller company who uses a travel agency instead of a portal system, is petitioning the company to order the agency setup a Continetal TA portal account - essentially a co.com website for travel agents to log on and book travel. Tickets booked through this system all earn 100%.