I have been pondering this and came with somewhat convoluted solution, worthy of fairly confusing name. Kontakt has multiscript feature, you can run scripts on MIDI level before MIDI data is passed to individual patches. You can change MIDI channel for events with multiscript. So my idea was to prepare sequence data at sequencer instrument level, in a way which would include channel/cursor number. Send it to another instance of Kontakt, where it would be decoded to multichannel sequence on multiscript level. Lets' see how it works...
Maybe it's not very practical, but isn't that fun? You can make it work with Cracklefield 1.2 or Orchestra Enigmatica, both of which generate a kind of multi-channel sequence and include a function which prepares data for receiver/decoder multiscript. They convert notes to series of CC messages, which include note number, velocity and channel/sequence number and can be then interpreted by receiver multiscript.
If you'd like to try it, download the receiver multiscript here.
Mind you, this is experimental setup, not guaranteed to work for you. Also you may need a bit of advanced know-how with Kontakt and DAW configuration, for example, know how to connect one instance MIDI out to another instance MIDI in. Read included text file for more information. Have fun.