And geology, astronomy and cosmology. Do you distrust them as well?
On the one hand, there is no complete record
There never is, whether one is dealing with archaeology, geology, cosmology or evolutionary biology. That is simply the reality. Rather than throwing up our hands and saying, "there isn't a complete record, therefore we can't draw any conclusions", we instead form the best hypotheses to explain the evidence at hand. These hypotheses are disprovable; a pre-cambrian rabbit fossil would disprove evolution immediately. So far, the theory of evolution is the best explanation of the evidence. Those who disagree are relying on the absence of a complete record as a means to disregard evolution are simply disregarding the evidence which is extant.
On the other hand, because it is treated as a blueprint for a whole range of disciplines which can be empirically tested (DNA, etc.) - the repeating challenge is whether the conclusions being drawn are "kluged" - made to fit the blueprint or orthodoxy of a presumed continuum?
It is treated as a blueprint because it is the best explanation for the evidence. Should a better explanation come along, the theory would be supplanted. It should be noted, further, that DNA evidence supports the theory of evolution.
Biology insists on a preferred status, an autonomy among the sciences
I see no evidence of this.
In my view, biology (et al) should become as epistemologically pure as physics and math - and not go into any investigation with presuppositions which are not required for the investigation at hand.
Biology and physics are not mathematics. And physics itself certainly is not "epistemologyically pure".
Drop scientific materialism ... to remove the presupposition of methodological naturalism.
That is the heart of the matter. Science should stop being science.
Science is a method for investigating material phenomena. It is concerned with what is directly or indirectly observable, testable and falsifiable. Supernatural causes are simply outside its purview. To try to turn science into metaphysics is to remove precisely what has made it so effective a tool for investigating and understanding the universe.
The third proposition does not neccesarily or logically follow from the first two. What non-circular reason is there to disqualify theories that invoke instances of agency or intelligent design? To assert that such theories are not scientific because they are not naturalistic simply assumes the thing in question. The postulate that there was agency involved in the origin of life and its diversity is no more outside the bounds of that which is directly or indirectly observable, testable and falsifiable than is the postulate of unobservable genealogical connections between organisms as the result of purely mechanistic processes. Presumably, you do not deny that it is possible that the actions of an unobservable agent could have empirical consequences in the present, do you?
Cordially,