mkvtoolnix. Take the track out of the MKV. As long as you have another audio track, it should be fine, although you can tell the output file to tag a different audio track as default (a good idea).
I never came across a way to strip Atmos or JOC audiopackets and metadata from their flatbed TrueHD or EAC3 stream. If it is possible somehow, I'd also like to know.
Same goes for extracting 5.1 AC3 core which (UHD)BD mandatorily carries in EAC3 (with or without JOC btw). To my knowledge, mkvtoolnix offers no "reduce to core" option with EAC3 streams.