Should the Scientology organization receive tax breaks from the British government?
Small local churches are often involved in their community and have very little money with which to perform their charitable works, and do make contributions as significant as non-religious non-profits. However, at least in the United States, it's far too easy for someone to found a "church" and get all the tax benefits and recognition as a religious institution while doing nothing for the community. And of course, there are larger churches that make what I'd call token gestures of charity; they have the cash flow of a national corporation but make less of an impact in peoples' lives than the tiny church down the block.
Ideally a church could function the same as any non-profit, but I doubt any church would want to deal with such a transition (and might fear for their legitimacy) regardless of whether or not they were part of the problem.