We don't do any churches but we do do some real pucker places with Victorian coloured leaded glass.
There is a difference between stained glass and leaded windows with coloured glass.
My advise is to stay well clear of proper stained glass as the 'stain' can wear off whether it be with ionised water or solvent based cleaners. I know this much to my horror a few years back.
As for coloured leaded glass, if it's old it will probably leak with WFP.
I've found the only real answer is to buy isopropyl alcohol, spray it on, and brush it on with a soft brush and then brush it all with a stiff brush to get rid of all the corrosion around the lead and then spend ages with a microfibre cloth.
With regards cost I always say it will be expensive as the time spent will be a lot but usually this is offset by the fact that it will only need doing every 3 months or so.
If any customer ums and arhs about it I say that it's best they seek the advise of someone who is a proffessional in that field. Usually, they phone us a short while later after finding out just what a proffessional with leaded glass charges.
Apart from that, I avoid antique leaded glass (if I can) like the plague.
Cheers