This is a complication that is specific to Americans because the US consulate does not authenticate documents. Other countries do, which makes the process much less painful.

Only option is to send your diploma off to your state to be locally authenticated, then to your state's State Department, then the US State Department, then the Qatari consulate in DC. Will take some time to get all this done.

Don't overstay. Fly out to Bahrain or Dubai for a week-end once a month until the mess is cleared up. Will only cost QAR 10 for you to get a visa at the border.

If your company is honest enough, they should pay for your flight as well.