The definition of proof depends on the context:
* Mathematical proof is a logical set of deductions based on a number of base axioms. As it is not emprical, we can achieve certainty
* In science there is no such thing as "absolute certainty," all ideas about how the universe works are subject to potential revision as new evidence comes to light. As Gould says:
"In science, 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional assent.' I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms."
The more evidence that is amassed for a particular theory, the less likely it becomes that fundamental changes to it will have to be made in the future. It is not about finding truth, but rather gradually approaching it.
Science uses methodological naturalism, it does not assume that nature is all that exists, but recognises that it is all we can reliably test. It could very well be that we all have invisible/intangible goblins sitting on our shoulders right now, but if we cannot test it, then it is not a part of science.
There are an infinite number of ways that the universe could work, but only one way that does work, and so the probability of determining this through faith alone becomes infinitely small.
I'll let someone else tackle defining what proof is in terms of society and culture
As for your first question: as the saying goes, absence of evidence is not evidence of absence. However that is not to say that there is no such thing as evidence of absence. For example, if you have a box, and a theory that there is a ball inside, then open the box and find no ball, this can be construed as evidence that there is no ball inside it

Also on a related note, keep in mind that when someone thinks are only two opposing theories, there are often actually many, and so evidence against one is not evidence for another.