The GPA is already less meaningful because of variations across universities and their overall grading policies (e.g. it's harder to get an A in a science course at MIT than at Brown but getting an A at either of these places is still harder than some no name state school with low admissions standards). The MCAT by its nature is standardized and thus inherently has meaningful value in isolation.
This is why schools select for MCAT scores and why top schools have high MCAT medians, even though nearly all schools have GPA medians of around 3.7-3.9.
Regardless, someone getting a 3.9 regardless of their major shows that they did well academically in college. If we want to assess their science competency, just see their science subsection scores on the MCAT and evaluate accordingly. A humanities major with a 3.9/526 (but did not take any science courses at all) is viewed to be good in sciences... but another humanities major with a 3.9/506 (with 124 in both science sections) might be recommended to take science courses to demonstrate competencies.
The MCAT provides a lot of information regarding an applicant's analytical and critical thinking skills, especially their ability to critically analyze science/research-based passages. That is more credible than making everyone taking prereqs without having any way to reliably assess the quality of those courses.
