I would be willing to create pull request - but it would be good to know how do you want this to be implemented. IMHO parsing is reasonably fast to just do quick fix - put the parsing method parseNativeQuery into synchronized block would be an easy fix.
Other option would be to call newInstance every time the parser is used. Not sure which one is better, but given the usual simplicity of the native query, I would go with the synchronized block. Parsing the query is imho just very small fraction of query execution anyway.