Yes, this is a problem and I am currently trying to wrap my head around a solution for this. It will probably use multiple (stereo or mono) audio files with the different mic positions for one zone, so in the sampler they will be treated as one sample but can be individually purged (and changed in the volume).
What I haven't decided yet is where in the signal path I should blend the mic positions. There are multiple options with different advantages:
1. Mix them together while reading from disk.
Pros:
very efficient and the multithreaded disk preload threads can be used for this.
the voice amount will stay as low as with one stereo channel.
Cons:
different effects on different mics is not possible (only volume and perhaps balance but no effect chain).
2. Keep the mic positions seperated until the FX processing
Pros:
You can use all effects with multichannel mics, and the routing can be freely configured
Cons:
basically you have the same calculation effort as using different samplers, but with less workflow annoyances (because it is only one sampler).
Currently I am implementing the first option, but I would like to hear from you guys what you would prefer.