I think the GPA suffers from significantly more confounding factors than the MCAT does. Despite how poor of an indicator it is to future success, the GPA is unfortunately the only tool (in addition to the MCAT) used to assess students.
GPA is an especially poor measure of things related to work ethic, academic readiness, etc. because it is so significantly variable from institution to institution...
Yet, when opponents are confronted with this argument, the argument basically comes down to "well, student A at rigorous institution X was able to pull off a 3.9, and student B at institution X was only able to pull off a 3.3", while completely ignoring whether they even studied the same majors, let alone took the same courses or courseloads, etc...
The major problem with this argument is that it says nothing about how student B would have done at less-rigorous-institution Y, where another student C at institution Y was able to pull off a 4.0 and get an equal or even slightly lower MCAT score and get into med school without any headaches. Obviously, we don't live in a perfect world, but there's clearly a logical fallacy at play here, and unfortunately student B gets screwed by the system.
Mind you, the MCAT is not perfect, but it's much better controlled and if a student is dissatisfied with his/her score, s/he can take it multiple times.