As with the aliens in 2001:A Space Odyssey, soldiers couldn't meet the strangers and blast them with a ray gun. They didn't exist on our brane. In Ben Bova's Jupiter the creatures living in the dense layers of gas on that planet had no connection to how life exists on Earth, either. This meant the story couldn't be about a direct confrontation between our species.
The problem with this is it's much easier to create conflict if an alien has arms and legs and can be blasted back to Orion with teflon coated gluon rounds. This is a real challenge in hard SF: how to create 'non human' aliens in human stories. Some will have them 'take over' human beings as in Dark City or any number of Star Trek episodes where the aliens speak through crew members which make them destructable. But in the above examples of Hoyle, Clarke, and Bova, they use the alien presence to create human conflicts without the alien being a direct menace. The alien may threaten life on Earth, but shooting at it won't help. The conflict is in how the human race will deal with the unknown.
It may be a while before mainstream SF moves past the 'space blaster' genre as the standard bearer. But we can still embrace stories that don't make warriors of us all when faced with an alien presence.
As soon as next year, the Large Hadron Collider at CERN may break the 16 GeV energy barrier and demonstrate the existence of the Higgs Boson particle. This isn't science fiction. This is hard science in Geneva. The Higgs is purported to exist in more than our 3 dimensions. If we distort, destroy, or tag one in any way, might we possibly be disclosing our existence to intelligent lifeforces that may share our space but not our dimension?
What do you think they will make of finding a particle that has been deliberately altered coming from a dimension of space where they thought no life could exist?