I'm not a Schoeps user but I believe the 41's are closer to your supercard definition in pattern.
I also like running a setup similar to SonicSound with 4 mics that I can mix after the fact (or not) to best effect, but I don't think that is necessary for a great recording if you don't have the gear or inclination to set that up. I usually use a spaced omni pair and a central directional pair, or sometimes four omnis in a row. In this case I'd consider the two omnis my primary pair and I'd have no hesitation running those alone for a simple 2 track recording.
The Williams charts are great and I recommend them as a starting point, yet I don't think they apply as strongly in this case as they would for other things. Two reasons why: 1) In this case the organ sound is sort of big, room filling and all encompassing and not sharply defined by transient attack of the notes. The primary goal of William's arrays is managing the recording angle distortion so that the playback image is accurately reproduced between the two speakers. That is more of a concern with things such as a group of acoustic players whom you'd like to image sharply and accurately across the playback stage, reflecting their positions when the recording was made. To a lesser extent the same applies to recordings of amplified music with FOH reinforcement. In that case reducing the image distortion within the image is less important than getting the width of the overall pickup angle correct. In contrast, in this situation the sound is less directional than either of those cases. 2) In my experience the Williams charts work best for directional mics. They also work for omnis, but for one thing, spaced omnis don't image as sharply which reduces the value of dialing in the most accurate imaging. Compounding that are other factors to consider which are often more important for me. For lack of better words, those factors are usually the 'timbre' of the recording and the 'stereo-ness'. The amount of spacing between the omnis effects both of those things. If you can use a pair of isolating headphones and monitor while setting up the mics with music playing you can adjust those to taste. Doing that I often end up with a wider spacing than Williams suggests, but not wide enough to make a hole. Often I end up around 3 feet / 1 meter. YMMV.
The Williams approach is a great starting point for the omnis though and clearly applies to a directional pair if you add them. A coincident or near spaced config with the mk41s would make a great second pair if you care to try that.