Theistic scientific explanations

In this post I will briefly consider two stock objections to the use of theistic explanations in science. Although I'll comment on their individual merits, my main objective will be to comment on their mutual consistency, or lack thereof.

1) Theistic explanations are a science stopper

If you don't understand how something works, never mind: just give up and say God did it.  Please don't go to work on the problem, just give up, and appeal to God (Richard Dawkins).
Don’t ever be lazy enough, defeatist enough, cowardly enough to say “I don't understand it so it must be a miracle - it must be supernatural - God did it”. Say instead, that it’s a puzzle, it’s strange, it’s a challenge that we should rise to. Whether we rise to the challenge by questioning the truth of the observation, or by expanding our science in new and exciting directions - the proper and brave response to any such challenge is to tackle it head-on. And until we've found a proper answer to the mystery, it's perfectly ok simply to say “this is something we don't yet understand - but we're working on it”. It's the only honest thing to do (Richard Dawkins).

One problem with this objection is that we could easily draw the opposite conclusion. For instance, surgeons act as if human body parts and organs have a purpose. That's the point of corrective surgery. To fix a malfunctioning part or organ. They treat the body like a machine. As if various parts and organs were engineered to perform specific functions. That's a presupposition of corrective surgery. 

2) The argument from suboptimal adaptation  

What I mean by bad design is the notion that if organisms were built from scratchy by a designer–one who uses the biological building blocks of nerves, muscles, bone, and so on–they would not have such imperfections. Perfect design wold truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution; in fact it's precisely what we expect from evolution. ..we should expect compromises: some features that work pretty well, but not as well a they might, or some features–like the kiwi wing–that don't work at all, but are evolutionary leftovers (Jerry Coyne).

One problem with this objection is that it suffers from an atomistic definition of optimality. It disregards the balance of nature. For instance, if predators were a little more efficient, they'd capture prey more often. Prey would be unable to maintain a replacement rate. As a result, both predator and prey would become instinct. All the prey would be eaten, after which the eater would starve to death. Conversely, if prey were a little more efficient, they'd elude capture more often. As a result, both predator and prey would become extinct. Predators would die of starvation, and so would prey–because of overgrazing due to lack of population control. 

However, my main point is to consider if these two objections are mutually consistent. Suppose we grant (1) for the sake of argument. But by that standard the argument from bad design is a science stopper. Since evolution predicts for suboptimal adaptations, a Darwinian doesn't expect "vestigial organs" to be functional. Doesn't expect "junk DNA" to be functional. He stops looking for a solution. He gives up before he tries. He simply defaults to "suboptimal adaptation." Once he classifies a trait as "suboptimal," he doesn't even try to find a better explanation. 

So these two objections cancel each other out. Both can be wrong, but both can't be right.