An interesting thread: I really ought to comment, even though the thread is rather old.
I have taken many photos of stained glass in France, where many cathedrals are open for the public. Many are supported financially by the public purse through the state and local government and are regarded as national treasures, though in many cases they are also used for church worship. Maybe because of the use of public taxes for the upkeep of such buildings, the authorities allow the public to take photographs without much sign of restriction.
In the UK, the ownership and upkeep of churches varies from one denomination to another. In the Anglican church, a parish church is the responsibility of its own council, which these days is a registered charity. The council makes its own policy on the opening of its church in the week, and access for photography. There is wide variation. Unlike in France, there is hardly any funding from the state for upkeep.
I am both a keen photographer and a priest, so I see both aspects at the same time. My own church has some fabulous stained glass windows by the renowned 20th century artist John Hayward. I have been trying to take some definitive photographs of each window for a booklet which people will be able to take away.
There are many issues with the photography of a stained glass window. People might wish to add to the following list:
1. The light entering the camera will have been largely transmitted through the glass from outside the building. There is generally little contribution from light sources inside the building.
2. The intensity of the external light varies greatly through the day and throughout the seasons.
3. The external light source can be as diffuse as uniform cloud cover through to an effective point source of the sun in a cloudless sky. In the middle is a wide range of source widths, with the sun reflecting off white cumulus clouds of various sizes and dispositions relative to the windows.
4. The height of the main source of light varies as the angle of the sun varies.
5. The lighting can vary rapidly on part sunny days: from second to second. This makes it very challenging to get a set of photographs with similar external lighting conditions.
6. Buildings, trees and hills in the vicinity can affect the external lighting falling on the window.
7. For some windows, the camera will see through the stained glass to trees and buildings at a distance. How much do you want to have the surface of the stained glass in sharp focus, and the external features out of focus? Shallow depth of field can be helpful here, but with a massive window to capture, you may find that only part of the window can be in sharp focus, as the camera needs to be tilted in order to frame the entire window - think of very tall buildings. Tilt-shift lenses can help here.
8. John Hayward used some very lightly coloured glass in some parts of the windows; and very dark indeed close beside. Additionally, the leading makes very dark lines across the image. The dynamic range of the scene is far greater than I normally see in landscape or portrait photography. I find I have to use exposure bracketing of several stops to cover the dynamic range, even on a Canon 5D MkII. The problem is the subject: not the camera!
9. Internal lighting falling on the inside of the stained glass can sometimes be a problem. If the windows have not been cleaned in a while, there is a lot of dust. The windows can look pretty clear with the external light coming through them alone. Switch on the internal lighting and the dust shows up, reflecting the internal light. This reduces the dynamic range of the image, reduces contrast, and can introduce a slight shift of hue.
10. The amount of lead (think dark stripes and crossing lines) in a window reduces the average light across the whole image. Depending on your metering system, the automatically set exposure can make the stained glass too brightly lit. You need to allow for this by stopping down a little. I find it best to take some test shots and look at the fine detail in bright and dark parts of the image, adjusting the exposure to get best balance. But you are fighting against changing brightness levels outside. Not easy.
11. There is so much detail in stained glass windows, that noise can be a significant problem. I tend to use as low an ISO as I can manage. In consequence you need a long exposure. This is not in itself a problem, as the window is thankfully still. But a tripod is very helpful: almost a must. You may need to have one with an extending pillar and use a remote control in order to get the geometry right. I sometimes use a self-timer to avoid camera shake.
12. External flickering can be a problem in some locations: think of a bright Maple tree outside the building, lit by the sun and a breeze blowing the leaves. You get lots of twinkling coming through the image. Consider what kind of result you are looking for, and allow for these effects in how you set your camera.
13. To get really decent images of stained glass windows is a fantastic challenge as there are so many tough issues to face up to. I have found that I can only get decent images from very good primes or L zooms. I also find the need to hire glass on occasion.
14. Finally: do you use a wide lens fairly close to the window, or a telephoto from far away? Much depends on the design of the building and decent access points for a photographer, but it is best to carry a fairly extreme range of lenses. I have found a need for 24mm at the wide end to 400mm at the tele end.
If you are a good photographer who can cope well with all of these parameters, you might like to consider doing a shared project with a church: to capture their stained glass windows at their best, and produce a brochure. But do remember that each church is subject to its own separate council/committee. Reactions cannot be predicted! They vary enormously, and often take ages to make up their minds.
One more thing: most people associated with churches are volunteers, going about their work without financial gain, and without charging for their expenses. They make their contributions for the love of their community and their visitors. I hope that may help explain why sometimes you get what seems to be a not very professional approach. It can help if you do a little research on who is responsible for the fabric of the building, and speak to them about your interest.
Hoping this helps stimulate some more interest in this thread!