The annoying thing, I feel, is that there are so many actual controversies in evolutionary biology that are infinitely more interesting than whether or not God had a hand in the creation of the universe.
While I do care about creationists lying about what I do for a living, I don't really care if there is or is not evidence for God or creation or whatever. The phylogenies I reconstruct, and the species I describe, and the evolutionary processes I speculate on work perfectly fine without divine interference, but would not change one bit if there was unequivocal evidence that it was all God's doing after all. There would still be evidence for colour-changing in peppered moths, and beak-size changes in Darwin's finches, and the loss of eyes in cave fishes, and all the other stuff. I would still get the same phylogenies based on the same data, and I would still find the same morphological differences between the same specimen. It simply does not really matter.
What does matter is that the focus is put on the wrong things. The world is wonderful, and animals and plants and physics and chemistry and geology and so on is awesome whether it's all God's doing or not. Pyrosoma won't stop being a jet-propelled sea squirt colony you can swim into, Symbion pandora won't stop having the weirdest life cycle known to mankind, the Rift Lake cichlids won't stop being amazingly diverse, scorpions won't stop glowing under UV lights, the Emperor Tamarin won't stop always giving birth to twins and signalling each other with their long, blue tongues, and Volvox won't stop being one of the most beautiful plants in existence (1) just because you add/subtract God to/from the world.
Even if we were to grant that discussions of God are relevant to biology, the "controversy" over his/her existence must surely be the dullest of all controversies in evolutionary biology. A top ten list of the greatest debates in the history of evolutionary biology would not include that of God's existence. Does orthogeny exist? Punctuated equilibrium or continualism (or both)? Can "ancient asexuals" exist, and if so what does that imply? Allopatric, peripatric or sympatric speciation? What about despeciation and respeciation? What is a "species"? Or a "genus"? Is there a difference between "parallelism" and "convergence"? Why does sex exist? Even the seemingly dull, but oh so prismatic, "Is a species a set or an element?"-debate is more interesting than the question of God, as is the (sort of still ongoing) discussion on paraphyly.
The list could go on for pages, without finding an controversy or an argument that is not both more intellectually fulfilling than the creationism/theories-based-on-data-from-the-real-world-and-actual-logic debate. These are all rewarding debates that would be interesting and relevant to biology whether or not God exists.
It may very well be that some god steered evolution to produce us, or even that everything was created to look as if evolution happened. The God hypothesis is after all just one step less parsimonious than any non-god hypothesis. But why does that matter in the least? Regardless of the answer to the question, "Does God exist?", we still have data which can be, and should be, sorted, analysed, and explained with non-divine methods.
You should be allowed to start your first lecture on evolutionary biology by just saying: "God may exist; he may also not exist. That is entirely irrelevant to this class. Now: do ancient asexuals exist?"
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(1) Note: This is an opinion.
