While I agree that it should be a late-stage hypothesis for simple Ockham's Razor reasons, there is absolutely nothing irrational nor supernatural about ET. Everything we know about life and about the universe, including the prevalence of Earth-sized and possibly Earth-like planets around other stars, makes ET an inductively obvious and very likely reality.
It's not confirmed yet, but it's a hypothesis that belongs in the same category as the Higgs Boson prior to the LHC: according to rest of what we know ETs should exist and we should expect to find evidence of this in some form someday.
It could come in the form of microbes or fossils on Mars, Titan, or Europa, or it could come in the form of a signal or even a probe or a spacecraft from the stars. The latter is IMHO no less likely. We exist and we send signals and space probes and pretty soon spacecraft. While we don't yet send these things very far, if we continue to develop as we have been we probably will someday. If we are a product of natural processes and those same processes are happening elsewhere (naturalistic metaphysics plus Kepler data says yes) then other things capable of sending signals or craft should exist elsewhere. Due to the age distribution of stars, some of them may have been around longer and therefore have had longer to evolve.
If anything the persistent absence of ET would suggest to me that modern science's fundamental understanding of reality may be incorrect. Either the theists are right, we're in a simulation (which is virtually identical to theism when you think about it), or something else profoundly strange is going on.
I attribute the intense skepticism of ETs to the silliness of much of UFO mythology. It's important to realize that the Rael cult and the abduction myth and so forth are a cultural phenomenon that has zero bearing on science one way or the other. Culture will take scientific ideas and hypotheses and run with them, and that's fine, but it shouldn't distract from reality or provoke an irrational backlash. Do we stop looking into "weird" possibilities in quantum physics because there are new agers who say silly things about QM? No, and we shouldn't dismiss aliens either. If we do we are actually letting pseudoscience and non-science dictate (in the negative) where science is willing to go.