simply kill the process this will not make anything worse. Remember that you also can run nsrck for one or more specific clients. without this option, it will check all clients. and as you see - this can take a while depending on the size ...  
I run a nsrck L6 command. However it's taking longer than I had anticipated. Would it be OK to stop the process. Or would it corrupt some client index files. Are backups OK to continue running while it progresses?
Stopping nsrck L6