The discrepancy has been raised repeatedly over the centuries, by scholars Jew and non-Jew, Orthodox or not, alike.
Rabbi Shimon Schwab penned an essay on it whereby he very much raised the possibility that the non-Seder-Olam chronology may be correct, though later referring to it as a "thought experiment."
In his taped lectures on the history of the Universe, Rabbi Yosef Gavriel Bechhofer at one point says something to the effect of, "while I hate to say this, it may be that we cannot always trust Chazal with regards to timelines."
The alternate chronology does not violate any of Rambam's Thirteen Principles. Here's more on what exactly "emunas chachamim" means, though note that the phrase does not appear in the Babylonian Talmud.
Personally I find an approach that casts Chazal in a negative light to be ... well not prohibited or heretical per se, but just plain distasteful. I'm okay living with "it could be Chazal are right on this and the secular sources are wrong ... it could be both are right and we've misunderstood the discrepancy ... and it could be that Chazal had valid reasons for listing a different chronology."