While some checking with your eyes wouldn't hurt anyone, doing it all the time will develop a certain habit - the one when you constantly have to look at your fingers and feet.
If this is happening to you also, you might want to pay attention to the following risks:
1. You will not know your keyboard and pedalboard well enough. This means you will have a difficulty finding the right notes on the organ without looking. This leads to more mistakes when playing.
2. Constant movement of your eyes back and forth to the score and to your fingers and feet divides your attention. Focused attention to the score (or more precisesly, to the measure that you are currently playing) is the key to engaging playing. If you lose focus, your listeners will lose focus all the more.
So how can you fight this natural urge to look at your fingers and your feet? It's a perfectly normal feeling because it feels risky to play without looking. So people look down out of fear of failure.
Or maybe they do so out of fear of fear of failure? That's right - fear of fear of failure. That's different. This is not an actual risk - it's the preconception we create in our mind.
Making mistakes feels bad. Feeling bad produces guilt. Guilt produces shame. Shame produces fear.
But it's not real. It hasn't happened yet. We just think we might make a mistake because you can't look at your fingers and feet.
So here's what I recommend: memorize your piece and play it from memory with your eyes closed for a week. This will feel weird at first - you will make lots of mistakes at the beginning. But towards the end of the week they will start to disappear.
Blind organists do this all the time - they can't see so they learn to feel the keyboard and the pedalboard. You only have to struggle for a week or so because after that it will become easier.