There are many problems with digital organs, even with pipe-digital combinations, that make them inferior to a genuine pipe organ. Many have been discussed thoroughly before. What it often boils down to is that electronic/digital organs do not last as long (some decades, if you're lucky) as their pipe counterparts (centuries, with proper care) do. Then there is the fact that a digital organ will never really be any better than a good recording, rather than a genuine sound with the epiphenomena that give it its real character. Tone colors also blend together. (I once played Messiaen's Apparition de l'Eglise Eternelle on a digital organ, and the stop changes were hardly worth my time; it just sounded like an enormous blob of sound.)
Another reason has made itself known to me in most inconvenient fashion (although to protect the well-meaning parties involved, I'm not gonna give any more detail that that): the volume levels and balances of the organ can be adjusted quite easily. Oh that may sound convenient. But it isn't, really. This means that someone else can change your sound palette without your being aware of it--until it's too late.
Yes, my friends, it's a week before Easter, and I might have to go back and re-do organ registrations. That wasn't exactly in my itinerary for the week.
Pastors, if your parish is in need of an organ, get a pipe organ, and if you don't feel up to the task of explaining to the congregation why they should contribute their hard-earned (and increasingly inflated) money toward such an investment, find a local organist. Most of us are quite eager to explain this to those who will listen. Don't listen to the salesmen that sell; listen to the organists who are responsible for making the music.
An additional thought: It occurred to me on my afternoon walk (with my new hat) that the only sound artistic reason to use an electronic instrument is to harvest its peculiarities, e.g. using a Hammond organ for jazz. Do you think that Eric Clapton, for instance (yes, believe it or not, I know who he is), would use an electronic guitar when he really wants to use an acoustic guitar, or vice-versa?
Precisely.