This should be fixed in Rigor Module v0.4.0.
This release fully fixes the problem of the bioassembler fully dying instead of being replaced by the "dead bioassembler". And this should automatically work for any other "living machine"; I checked out the incubator, but as it has no recipes that accept rigor modules, the incubator can't accept rigor modules at all (but if it did, the fix would work for it too!)
There were also a few lines of extra compatibility code I added (so that rigor modules would stop dropping on the ground when bioassemblers turned into dead bioassemblers) here.