The short answer is Yes! Over time it will screw up your piano playing. The real question is whether the church will pay you properly and employ you as an organist in the future.
I respectfully beg to differ. I was, for many years, a Minister of Music, and my college training was as an organist. I also, however, play piano; I'm not sure which one I play better, but I still play them both.
Where the problem as regards technique comes in is if you regard the two instruments as somehow the same because they both have keyboards. They aren't the same. The technique -- even to the way you hold your hands and fingers -- isn't the same. Fingerings can be quite different for what looks like the same passage (I sometimes use, for example, right hand 2 3 4 5 3 4 5 3 4 5 etc. for an ascending scale on the organ; a pianist would be horrified!). The approach to phrasing and voicing is different. Never mind such details as using the pedal keyboard with equal facility to the fingers, or the subtleties of registration or when (or most often in baroque, when NOT) to use the various swell pedals.
Etc.
If, however, you will approach the two instruments as being completely different, and make no real effort to transfer one to the other, you'll be just fine.
Further, allow me to point out that there is more to being a church organist than just sitting up there and playing the hymns, although that is a very important (and actually the hardest) part of the job. There is also the selection of music for preludes and postludes and, commonly miscellaneous service music, such as an offertory (if you don't have a choir). Then there are weddings and funerals, which can be wonderful but can also be absolute nightmares. You should have a really solid command of your church's faith and liturgy, and the church calendar (if your church uses one). And so on...
You mention pay. You will never get rich being a church organist or Minister of Music. For that matter, unless you should happen to be in some mega church in Los Angeles, you'd not get rich being the minister, period. Don't expect to. On the other hand, you can -- and should -- expect to be paid reasonably for the time you put in. And that, of course, is widely variable. It can be a full time position, although that is unlikely without a choir school. It can also be as little as 5 to 10 hours per week.