Yes. We would do this by analyzing their arguments for logical errors, then testing their new theory, then hopefully proving their new theory. The difference between a crazy and genius is the results their new ideas produce.
In Ramanujan's words, "an equation for me has no meaning unless it expresses a thought of God". In mathematician circles of the early 20th century, this was an obscene statement. Even today, can you imagine a researcher in any field saying something like that, and being taken seriously?
Yet Ramanujan is probably one of the greatest mathematicians of all time. In Hardy's word, he had "never met his equal, and can compare [Ramanujan] only with Euler or Jacobi".
To think that "we" (whoever you mean by that) can recognize sheer talent of Ramanujan's type is, frankly, arrogant. If anything, the ivory towers are even more enclosed - research is more and more about the quantity of publications, not about the quality of ideas. A recent Nobel Laureate stated that if he had not received the Nobel Prize, his university would have probably fired him, for lack of a consistent publication record.
So no, I don't agree with your statement. While the scientific method you describe for approaching nature has worked tremendously well for understanding the world, it still completely fails to capture the core of what it is that makes a person a true genius.
After seeing Ramanujan's theorems on continued fractions on the last page of the manuscripts, Hardy said the theorems "defeated me completely; I had never seen anything in the least like them before", and that they "must be true, because, if they were not true, no one would have the imagination to invent them".
I'll agree that the costs don't come close to replicating work by LIGO or CERN.