Certain InTel features like the profiler, the performance advisor, and the real time performance panel consume both the output from $currentOp and slow query logs. It would improve the user experience of these if we could easily filter out internal operations. I think it would be easiest if we simply added a boolean field to each entry in the output of $currentOp and slow query log lines (and the profiler) indicating internal operations.
It used to be the case that user operations could be identified by matching the thread name to "conn####" but this is no longer the case in newer versions of the server.