Ok the whole of the OP is just stupid. Things researched now seem to be funded on the basis of the return in the short term financially by companies who want to see bang for buck from researchers, a lot of research that isn’t going to directly benefit us in the short term often has to be financed by private people, or companies, or x that want to explain certain things that they know will be unlikely to have a financial return. Science is already a capitalist system, sadly.
The thing is though there are certain things that might not benefit us straight away that some companies and financiers see as viable as the long haul may well give us sustainable technologies that will simply revolutionise human existence. CERN is one of those things that most people think well what is it going to do to benefit mankind in the next 20 years, probably nothing, in the next 1000 probably everything. Science isn’t totally beholden to business in the short term, because business in the short term are fucking morons, who have screwed up the economy in ways that are far to long winded to go into now and don’t matter, but you get the point.
You can no longer seperate government from science, because most of government is utterly reliant on it, many companies have funded tech that brings in not just their source of money but keeps them in government. You might as well try and separate your head from your body and hope the system will continue to function.
Ludditism is all very well, but you’re sitting here right now relying on a system that is so intrinsically tied to government now for you to be doing anything in the modern world that separating them is a non sequitur. This is why war is no longer a viable means to promote technology, in times of war science budgets suffer, we can now do everything in labs we once had to do in the field by firing cannons at people we didn’t like. Get used to it, science is here to stay.
Should science be beholden to government no, is it yes. The good thing is as already said is government is so invested in science for the future survival of mankind in any state that does not denote widespread collapse of the system, that it cannot but be its lover.
People who make analogies between science and religion really have no idea what science means. They are about as useful as kine in a herd meeting out ideas on the basis of their ability to follow blindly another ideology. Worthless. Science is a paradigm, but it is the only one that says, that which tries to kill us and ruin our foundations on a rocky sure are the only people who are worthy of science. No other means of progress in history has been so utterly able to be overthrown by logic and reason and no other means of reasoning has seen so many heroes by simply destroying the mediocre meaningless exactitude of those chancers who thought they had the answer, and for grace and for goodness, for that we should not praise it, we should just watch it, like a hawk watches its prey and if for want of failing we descend on it like a hawk and kill it dead, so that a better phoenix may rise from its ashes in which it should lie buried. The king is dead, long live the king. 
“Science is but one death after another.”
Niels Bohr.
The same cannot be said of any other medium in history. It’s a good place to be science these days, because everyone is trying to kill everyone else, because for once in our history we have finally perceived the breadth of our ignorance, and like any good pack animal we see our chance to kill every other pack, but the spoil is not to feed on another pack, we don’t actually kill each other we work together, for once it is in our means to become one great pack, by using competition co-operatively. 
