Honouring Chazal

In the current battle between the rationalist and anti-rationalist groups within Torah observant Judaism, one argument continues to be raised by the anti-rationalist side that the rationalists seem not to have effectively rebutted.  The anti-rationalists contend that by casting doubt on Chazal's wisdom regarding science and other non-halachic matters, the rationalists are engaging in heresy.  Since the anti-rationalist view is that Chazal, in addition to their superior knowledge of halacha, also had ruach hakodesh in all other areas of knowledge and therefore their statements on anything are authoritative and considered must-believe for Jews, rationalists are outside the pale of proper Jewish belief by doubting the accuracy of Chazal's knowledge in this area.
The rationalists have not helped their cause by allowing the anti-rationalists to frame the terms of the debate.  The argument inevitably starts with the anti-rationalist side declaring that Chazal are infallible.  This forces the rationalist side to respond that, in fact, Chazal were fallible, leaving itself open to shouts of "kefirah!" After all, it's a slippery slope, isn't it?  If one thinks that Chazal were fallible in matters of science, then it's quite plausible to accuse one of thinking that their grasp of halacha was imperfect.  In addition, the anti-rationalist side has worked hard to create the impression that a literal reading of certain parts of the Torah which simply cannot be understood in that simplistic fashion is in fact the only way to read that part of the Torah and that such a method is a principle of the faith. 
All of this is a shame since most of the anti-rationalist positions are either indefensible or laughable, as these two short videos demonstrate.  When anti-rationalist positions are challenges head on using valid Torah sources, the only rebuttal seems to be "Well that's not what the Gedolim said so you're a kofer!"  Personally, I stopped using arguments like that around grade 6.
The solution to this problem for the rationalists is to aggressively reframe the debate.  Both sides agree that Chazal were great men who had a supreme knowledge of Torah that we can study and analyze but not improve upon.  We cannot know more Torah than them and they limits they set remain valid for our halachic analysis to this day.  However, the anti-rationalists have created a new image for Chazal, one is which they have become omniscient demigods with magical powers to turn people into piles of bones at will.  They believe that this is the best way to honour Chazal.
Therefore the rationalist position must be to challenge this head on.  Were Chazal supernatural beings, or were they great men with a desire to know God's will within the parameters of intellectual truth?  In short, if they were confronted with the fact that lice do not spontaneously generate from sweat but hatch from eggs like every other known insect on the planet, would they obfuscate with terutzim like "Well, nishtaneh hatevah" or "scientists are all liars" or would they re-examine the issue and learn about the new knowledge that postdated them?
When it comes to halacha, there can be no questioning of Chazal's authority.  When it comes to science, one must apply the standard that holds true in that field today, one of intellectual truth.  A real scientist, when confronted with evidence that opposes a theory or hypothesis of his, either tries to prove to contradictory facts wrong or adjusts his theory in light of the new information.  It should be the rationalist position that Chazal were men for whom truth, the seal of God Himself, was the overriding factor in their investigations of the natural world.  What they recorded in the Talmud was a reflection of the scientific truth of their day.  Had they been aware of other facts, like the size of the universe, the age of the planet, etc. they would have altered their views since truth is the overriding objective they were searching for.
For the anti-rationalists, Chazal are like global warming advocates who pick and choose the "facts" that fit their predetermined thesis.  The rationalists must oppose this on the basis that Chazal wanted honesty and facts as best known at any given time.  Thus a statement of Chazal that seems scientifically absurd today does not mean they are fallible.  Given the information available at the time they came to the most honest conclusions possible.  With the advancement of knowledge of the natural world and the development of the scientific method, we honour Chazal best by learning honestly about the universe around it and seeing how the Torah reflects itself in it since both are creations of God.