I've recorded organ with 2 x MK 41 but it's not usually the ideal choice. Among Schoeps capsules I would choose either the MK 21 or the new MK 22 as a starting point. Stereo recording is an "idiom"--listeners have expectations, and for organ recording precise localization is not so important. Giving an impression of great spatiality, dynamic range and frequency range on the other hand is nearly the whole game.
Where low-frequency response is concerned, I'm in the rare position of agreeing with the people who say that the spec sheets miss the point. The MK 41's low-frequency response is quantitatively adequate for organ recording, but we'd have to get into a discussion of standing waves and the way bass "builds up" in a room over time--the key point is that the propagation mechanism behind some of the things we hear at low frequencies, that are very important cues to the kind of space we're in, occur in a way such that highly directional microphones don't tend to pick them up very well. And people who listen to organ recordings tend to like hearing those phenomena on a recording, and miss them if they're under-represented.
--best regards
Edited later to add a P.S. for "SonicSound": The MK 41 and MK 41V are situated between the two classic patterns hypercardioid and supercardioid, but are closer to supercardioid. At 1 kHz the 180° response of both capsule types is about -11 dB relative to the respective 0° response.
This wasn't always the case, incidentally; the original MK 241 capsule of the M 221 series was closer to a true hypercardioid. But listening tests with customers showed that a pattern closer to supercardioid was preferable in actual use, so a change was made. It occurred in the mid-1970s, during the period of overlap between the later CMT-series microphones and the earliest CMC-series (Colette) microphones. It's actually not hard to tell which is which, because the "null" in the pattern is constant across the audio frequency range.