Hello Thomas,
Recording at the highest level for each stop should potentially give you slightly higher audio quality, and so should potentially make for a slightly higher quality sample set. However, if you do that then it would be important also to make a brief reference recording to compare the levels of each of the ranks (e.g. also record the middle Cs for each rank all at the same level), or at least to note down the recording level settings in decibels when each rank was recorded, so that you have the necessary information to reconstruct the original ranks' amplitude relationships within the organ definition settings.
If recording in 24- or 32-bit (which would be highly recommended anyway, since it gives plenty of 'headroom') then the difference in quality may not actually be that significant compared to recording everything at the same level, especially since turning up the recording level will also usually amplify the blower/microphone/electrical/pre-amp etc. (often approximately equally). The dynamic range and noise characteristics of the microphone and mic. pre-amps are likely to be much more significant.