okay, i"ll try answer soem of them.
If anothe civs agrees to convert to your religon - and you are the first to discover that religion -then you are one step closer to achieving a Relgious Victory. Its True - the cities don't go over to you - but you are one step closer to a Relgious Victory.
Seconldy - lets say you have converstion units as oppossed to conquering units. If you convert a city with a cleric unit, that city will go over to you. The advantage to converting a city rather then conquering it is two fold -or manybe even three fold. Lets say you ddidnt get to build the King Richard Crusdas, but rather the Peaceful one, therefore delcaring Holy War is not an optin at the moment - also, any one who attacks you will get bad repuation damage - so you deciede to convert cities. Firstly when you convert a city, it comes over to you wth all of its citizens (static mode) or alot of its citizens (dynamic mode0 the same religion as you - and therefore no or hardly any civil unrest. IF you conquered it by military miight you would have civil unrest and such, tand the citizens of that city would be unahppy untiil you stopped fighting their home Civ. Finally, you just gain a city - with out using any gold as well as not having to go to war or risk your reputation or risk losing any off your own cities.
(Just EDITED) furthermore - when you convert a city with a cleric unit that city come to you intact - no builidngs destroyed, nothing burned, no civil unrest, no risk of going to war, no cost of gold to you, no risk losing repuation, and no risk of you losing cities as well as gaining a city and being one step closer to a religous victory if you were the first person to discover that religion.
how the converstion numbers would actually work -I'll be honest with you on that dh - I'm not that great in that area - I'll leave the maths to others who are better talented then me. But i'm sure it could be worked out.
You're last point -which is a really good one, darn - I even like it alot - what is to stop a civ who just converted to your relgion after it made peace with you in your Holy War? I don't have the full answer yet - but I know there is one, part of the answer is - maybe the civ you where fighting when it agrees to convert to your religion - automatically sells all of its religous buildings - therefore if it converts back, it will have none of the advantages it had before. But it might do it just to stop you from having a Religous Victory - I know that's what i would do if I had to, I would convert just to give me some breathing space, and then when I was ready - to stop you having a RElkgous Victory I would change my religion.
It's a real good question. There is an answer for it - and when we find it, it will kinda of click everything together.
P.S. - how does opposing nation fight converstion. One option could be to place its own cleric units in each city on guard duty - like counter converstion mode, making it harder to get converted. Also, by increasing your own culture points and building loads of religous buildings and such, it wil make it more difficult for your people to get converted. Also, as with goverment types - certain types will make it harder or easier for your people to get converted. Final option is to declare war - when you declare war I don't think the other civ your at war with should be able to convert your cities.
When you win a Holy War - you can get a tremendous Reputation or Religous Points/ culture points boost, it also brings you closer to a Relgious Victory.