volvie, your reasoning is the crux of the problem. Undoubtedly, the Gra is heavens above us, but if you maintain that the chachomim are infallible-and this applies not only to the chazal,because you attribute infallibility to EVERY godol ,including our generation-then no one has the right to question anyone who is a godol and the Gro cannot make these comments about the Rambam, especially as they pertain to Torah matters, matters a lot more important than scientific facts.
The fact is that, in general terms, acharonim (including the gro) did not dispute the HALACHIC superiority of th rishonim. They did, however, dispute the every day opinions of earlier generations because on that, they were not infallible.
You cannot accept criticism of a later godol if you think that EVERY word of an earlier godol is infallible. The words of the Gro on the rambam are proof that the Rambam was NOt considered infallible by the Gro and it is preposterous to say that the gro was like a rishon. In greatness, maybe, but in fact he would not dispute any rishon on halchic matters.