I think it is a bit strange to ask "could science 'discover' meditation completely independently of a religious context?". Given that meditation is so common in eastern practices it seems unlikely that science would ever be needed to discover it - someone else is likely to stumble upon it first. If it were rarer than that, however, I'm reasonably confident that science could discover it. Given that science is all about discovering how things work, learning the quirks of the brain and consciousness is high on the list of things to do.
To flip that question on its head however, perhaps we should ask "could religion discover gravitational waves independently of a scientific context?". I would be very hard pressed to answer anything other than an emphatic "no". Indeed only a few hundred years ago you were probably likely to be imprisoned or killed for suggesting much less.
In terms of how long it took science to find meditation worthwhile - not long at all. Science is new. It wasn't until recently that we had the tools to be able to study the brain and study meditation. Any delay in attention toward meditation from then on may well be due to a bias against religion among scientists - but then so much of religion can be explained away leaving the signal to noise ratio so low it's unlikely to be of any interest to many scientists anyway. You don't go shopping for motorcycles in the grocery store. No doubt western religion itself would have contributed to delays though anti-eastern religious bias as well.
Of the people that are interested in religion - psychologists, neuroscientists, social scientists, historians - I have no doubt that they are already interested in it for all the reasons mentioned in the article. It's not as if religion is such a small part of our lives and we need to go digging to uncover it's secrets.
I very much doubt that there is any scientist out there whose area of expertise abuts religion that is inclined to disregard the entirety of religion as irrelevant. Richard Dawkins himself - quoted in the article - recommends that everybody should read the King James version of the Bible as a piece of literature and an important text culturally [1]. There just happens to be very little reason to bring along the hocus pocus with it.
[1] https://www.theguardian.com/science/2012/may/19/richard-dawk...