The US government has spent trillions of dollars building nuclear weapons for a war it never wanted to have. Think of Prometheus as a defense project. If aliens came, they would be far more advanced than us, and they might be conquerors, so it's a matter of self-preservation to prepare for them. By that thinking, cost would be no object. Or at least, the defense contractors who would profit from Prometheus's construction, and the senators and congressmen whose pockets they lined, would argue as much.
Besides, given all the missiles and planes and such in the stock footage at the end, I'd guess that the facility was actually a pre-existing, perhaps decommissioned military base that was chosen as the containment site for a potential ET because it was sufficiently secure and isolated.
Never underestimate scientists' capacity for tunnel vision. It takes many years of singular focus to become an expert in a scientific field, so that singular focus becomes a habit.
Besides, their job is to look for aliens. Gamma mutations are somebody else's responsibility. Would you expect an electrician to offer to fix your leaky faucet? No, they'd just tell you to call a plumber. It's not their department. And Hulks are not Prometheus's department. Abstract curiosity about all things in the universe is all well and good, but actual working science is a job like any other, and if a problem isn't in your field, then you let someone else deal with it.
On top of which, Prometheus is top secret. Not just because of the extraterrestrial and defense implications, but because a lot of voters and reporters might feel the same way you do about the justifiability of spending so much taxpayer money on a speculative project. So it would risk their secrecy to get involved with something as (relatively) public as the Hulk. Indeed, that might be why they didn't sic the military on the Hulk -- because Prometheus was so tip-top secret that even most of the military wasn't cleared to know about it.
That doesn't follow at all. If that were what they were interested in, then it would be a project for studying human superpowers, and the Hulk would be right in their wheelhouse. There's no reason why the existence of transhuman or supernatural phenomena on Earth would prompt a project to study extraterrestrials; that's as profound a non sequitur as, say, organizing a mountain-climbing expedition to study giant squids in the ocean depths.
You have to remember, this was the same generation that went to the Moon. The space race was a huge deal in the '50s through the '70s, and there was plenty of attention on space and plenty of belief that our advancement into space would be rapid -- and that included the belief that first contact with aliens had a good chance of happening within a generation or two. That's why UFO sightings and delusions were so widespread at the time, and why they were taken seriously by the government with operations like Project Sign and Project Blue Book. "Prometheus" came out in 1980, only 3 years after Close Encounters of the Third Kind, and a year after Skylab fell. Space seemed closer then, contact with aliens more imminent. (Note that it was also around 1979-80 that the myth of the "Roswell Incident" started to appear. Which is why it wasn't included in CE3K's UFO lore.)
