If using the system caused a major version update of node.js (which it seems it did) then you have to go into the .node-red folder and run
npm rebuild
so that any compiled modules are rebuilt. Unfortunately then I guess you will end up with the same problem you originally had.
Normally after updating node.js you would have to re-install node red so it is also rebuilt, but I imagine the system update did that automatically. It is in order to avoid this sort of problem that the install script I linked to is provided. That won't help you with your original problem though, the node needs to be updated. Have you submitted an issue against the node?