Hi,
I can’t give you any advice about creating samples, only about pipe organs and using sample libraries from the perspective of a player.
The sampler used in most professional software environments is probably hauptwerk (the software itself is free, hauptwerkshop.de, you have to buy sample sets though).
Organs have registers that can be used in arbitrary combinations - which is usually pretty difficult to model in standard samplers.
Hauptwerk sample-sets usually have samples for every single key and every single register, so you can combine them, as you like. In, say, Kontakt you could probably only have some preset registrations.
I think you would record your samples as dry as possible and put some software reverb on it afterwards, which you can then adjust to your needs. Hauptwerk does a decent job there, but I can’t tell you much about what format they use and things like that, probably they have documentation for that.
It depends though, what you’re trying to achieve with your sample set. If you just want to have a typical authentic organ sound as a playable VST or sampler, you coul as well go for a simple solution and record a pleno registration, lets say principal 8’, 4’, 2’ & mixtur, in a reasonable distance where you can catch all sounds in about the same volume and with room reverb. So if you don’t want to simulate a real organ with different registrations, multiple manuals, a pedal with its own sound, it still could work fine.
I did several organ recordings with a portable recording device. If you have a good one which can handle enough external mics, it’s not much of a difference to a laptop and audio interface. Cheap audio interfaces don’t necessarily have a better sound than good portable recorders.
If you have external mics you will probably set it up far enough away from your laptop anyway, so it’s maybe not a big problem. In my experience, churches can be pretty noisy places, there can be a lot of sounds from outside, like cars, people, airplanes, cats, motorbikes are the best 
If you’re in a city or near a busy place or street, your laptop noises can pretty quickly become one of your least worries
First time I did this, I spend a lot of thought on how to do it best, where to get the best microphones and recording equipment, but in reality, with two microphones for about 100€ and a decent field recorder you can get pretty good results. In my situation for example the bus that comes every 15 minutes is a way bigger problem than the little extra quality I could get out of better equipment.
A lot of those problems are gone if you record from very close distance. But it will probably take way way more time to do so, you would have to crawl inside the organ and reposition your mic for every note, this can take days.
Ok sorry, I’m all over the place without any structure to what I’m saying & I don’t want to discourage you.
Maybe I would try to first start with a very simple sample set, to get into the subject and gain some experience, if it’s a small or middle sized organ put your mic maybe 5-10 m in front of it and try a sampler that’s easy to handle for the beginning.
After that if you decide you want more professional results you can look into hauptwerk and maybe start with one or to registers to again gain some experience, what distances are good, what record settings etc.
I hope anything of this makes any sense to you. Organs are pretty complex and it isn’t as simple to answer as maybe for example when sampling a xylophone or something a little more consistent.
Good luck and have fun, organs are great