Don't know what you base such an assertion upon; but, never-the-less, true airspeed at lower altitudes is less and fuel consumption is greater (as well as in the climb) - all of which diminishes the overall efficiency of the jet, thereby - in this case - lessening its range.
From news reports that that is what it did. From the Daily Telegraph: "Signals recorded by the Malaysian military reportedly show the plane ascending to 45,000ft, well above the 777’s approved altitude. The same data suggested the plane then descended to 23,000ft as it approached the Malaysian island of Penang, but then climbed again and flew northwest over the Strait of Malacca."
Plus....it just makes sense. If you go through this much effort to get a 777ER...and you know enough to disable the ACARS (like maybe the pilot or co-pilot)....then you know you can't fly at lower levels without slowing down and burning more fuel. I'm not a pilot and I know that much.