The baby will change everything for the parents. That's normal. It would be selfish to let the spouse raise the child while you play the organ for long hours. However, in the long run it's crucial for both of the parents (and for the baby) to keep up personal interests and hobbies alive even for 10-20 minutes a day. You can of course take turns attending the baby.
If organ playing is your hobby, this well might mean you keep continue playing the organ. This activity will help re-charge both of you when you feel exhausted, when your energy level is down, when your spirits are low.
To help you see why it's important to continue your organ playing journey (if it's important to you in the first place), let's take an example of another sphere in live - piloting the plane.
When the plane flies from place A to place B and there is a high turbulence and a storm coming in front of the plane, the pilot normally wouldn't turn around the plane and stop the flight. No, the pilot would re-adjust the course, maybe turning left or right which would eventually allow the plane to reach it's destination by another route.
Sometimes the plane has to land to place C and wait there for better weather conditions. Then the trip will last longer but the plane will arrive to its destination nonetheless.
Here it's important to point out that sometimes the pilot doesn't fly at all. The pilot waits on the ground for better conditions to fly.
The same is in live. When life gives us expected or not expected challenges, we can re-adjust our efforts, re-adjust our schedule, re-adjust our priorities. But if your goal is eventually master some aspect of organ playing, you can do little things that matter most in the long run - short daily practices of 10-20 minutes of duration.
If you take a table spoon and try to dig a tunnel for 10-20 minutes a day - in 5-10 years you will move a small mountain this way.
Having goals and the purpose are very important here. Without them it is impossible keep going in baby steps and eventually to reach your destination.
Besides, keeping up the hobbies of both of the parents will be very beneficial to their baby, too (in the long run). This is because he/she can follow in the parent's footsteps. Also seeing that one of the parents is practicing something, this will teach the baby something about the value of waiting, the value of effort, the value of commitment, the value of delayed gratification.
People who grow up as selfish human beings sometimes saw the unconditional attention of their parents in the past, acting as servants. They expect that others will be servants to their needs and wants later in life, too. That's why it's important you also have your own time, too. By the way, this will only make your family bonds stronger.
Yes, this would probably mean you should practice at home more than at church.
This could also mean, you might practice more away from the instrument - on the table or even while lying in bed with your body still and your eyes shut (I once prepared for an entire recital this way). This could also mean you will value your available time so much more than before and accomplish things faster.
Don't turn around your plane. Adjust the course.
[Thanks to John for inspiration]