There are a lot of mysteries from the ancient world that have yet to be solved and if the truth behind those mysteries are discovered then it could destroy the foundation of everyone's belief structure. Once that happens then the world will descend into chaos and nobody wants that because it will be bad.
While it has been a long beheld belief that the pyramids were built using slave labor, it is entirely possible that the lead archaeologist has gained new evidence to suggest otherwise. Hopefully, at some point, the findings can be revealed and the discrepancy further explained. There may be a perfectly valid reason why they are coming to an alternative conclusion.
I do not think that the Egyptian government is covering anything up. I think that at this point, our understanding of the ancient world is still very limited, with new knowledge uncovered and new discoveries made each and every day. The new information that we gather with further exploration uncover new details and new understandings of our ancient world. Discoveries such as this one in Egypt are not a matter of covering up knowledge that we've had all along, simply making new discoveries and building upon previous theories and ideas we have about the ancient world.
Perhaps it is my own lack of knowledge that I must disagree with this question. Regardless, there are no previously cited indications that the Egyptian government has made any mention of the source of Egypt's ancient monuments. The fact that archaeologists have discovered tombs that indicate that the root of the monuments are not in line with the current working theory has little to nothing to do with the Egyptian government. With the limited information, the two subjects seem unrelated and thus I have no reason to believe that the Egyptian government is covering up or withholding information.