I shouldn't post this, but I will : ) Shu"T Binyan Shlomo (mentioned in this post before Shavuos) has a birchas hachamah tshuvah that is filled with interesting side tidbits. Among them is his discussion of the gemara's statements that refer to the sun travelling behind the world (Baba basra 25b, see Jewish Worker's post on this sugya) and other such ideas that scientifically make no sense to us. As everybody living today knows, the earth revolves around the sun. At the end of the day it becomes dark not because the sun vanishes behind some kind of screened off area in the sky, but because we are turned away from its rays. If you need any more proof that Chazal got the facts wrong just turn to Pesachim 94 where the gemara quotes a debate between the Rabbis and the non-Jewish astronomers and concludes "ni'rin divreihem m'divreinu" -- it looks like they are right!
Yet, apparently in Vilna it was not the practice to just toss out gemaras as "wrong" even where the discussion revolves around scientific material. R' Shlomo haKohen quotes the Rada"l's citation of Ramchal who explains that when Chazal speak of the sun or the stars or other heavenly bodies they were not discussing the physical bodies we call sun, moon, and stars, but were discussing the pnimiyus of these phenomena, their spiritual source in the world of sefiros. The GR"A in his commentary on Sefer Yetzira explains that this is exactly what the gemara means when it says "nir'in divreihim", it looks like the non-Jewish astronomers are right. Of course that's how it looks if all you see is physical reality and think that's what the whole discussion is about. Chazal, however, were speaking on a different plane entirely and discussing in their cryptic language the spiritual essences of reality and not the physical phenomena. (This is essentially a more sophisticated version of what R' Akiva Eiger alludes to in his Gilyon to that daf).
Apologetics? Bad pshat? I'll leave it to you to make up your mind. But consider this: if Chazal could be wrong about science, then why did R' Akiva Eiger, the GR"A, the Ramchal, the Binyan Shlomo and others need to say anything? One sevara (Chazal did not know science) answers all the kashes -- but that's the one sevara that these achronim assiduously avoid saying.