The impact on organized religion from extra-terrestrial visitation may not have materialized - yet - but the same impact can be gleaned from recent developments in computer science, nanotechnology and biotechnology/genetics.
Why does the idea that neuroscience, genetics and perhaps other fields - with their incredible complexity -have programming at their core, and show evidence of our brain or our DNA having been "intelligently designed" - buoy conventional fundamental religions?
If anything, this evidence would suggest that our anthropomorphic concepts of an angry (or loving - evidence of that?) gray bearded all knowing guy in the sky is flawed and outdated.
What this evidence might indeed suggest, instead, is that the natural universe is not an accident but that its source of creation and the laws that govern it are far beyond our comprehension.
What it may well indicate is that our senses are constrained and limited in their ability to comprehend reality, or that we must rethink our very concept of mind, matter, spirit, energy and particularly intelligence.
Humanity's invention of the computer (which has led us to the concept of programming and its mathematical principles as a living metaphor) may just be a fundamental step in our evolution from primitive mob driven religions to a deeper understanding of our true place in life -- with the realization that its mysteries are far deeper than previously thought.
As we discover evidence of programming (i.e., conscious reproducible instructions) in genetics and neuroscience (which would have made no sense before the Enlightenment and advent of technology) we need to expand our cosmology and religious concepts accordingly.
For one thing, the level of sophistication of the "program" that suggests that all life is indeed intelligent (or created) makes it obvious that the level of knowledge and power of whatever created life (since we can't) and programmed it in ways we are just beginning to comprehend is of an order of magnitude higher than anything we can even remotely fathom.
Calling this God without a scientific definition based on empirical evidence in line with modern science is ultimately meaningless. It is like assigning it an ultimate variable for which we have no value.
From this perspective, organized religion seems to be like the musings of an ant living in a giant garden or a huge estate in pontificating about the true nature of the king or president of the country in which the estate is located - so far removed in level and knowledge that all of its prattling is idle chatter.
What the presence of a mind (or an incomprehensible intelligent energy or force) behind life at its core (in the brain and in the genes) suggests instead is that our brain is limited in its capacity to even understand a fraction of its true nature.
If you have any doubt about this, go outside at night and look at the stars and try to comprehend the vast distances they represent. Then try to think outside of that space.
You can't. If you could, you might begin to understand the meaning of an intelligence behind life.