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Hey, thanks for the fast reply!
I was thinking about two quick n dirty ways to fix the problem...

1. Creating/Using a soundfont that does not do anything and putting it on all channels that i want to "mute". How to make or get it?
2. There are settings in qsynth that allow to create multiple output channels for jack. I dont know exactly how it works, but would it not be possible to tell qsynth to rout the sound produced by midi channel 2 on this jack channel. But instead of connecting it to the system, I just leave them unconnected.

However,
you are doing a great job on qsynth and qjackctl. Keep on rockin'! ;-)