Many battery powered scopes have insulated BNC connectors. This is the only safe way to go, in my opinion, since there is no way to ensure that the reference lead is at a safe potential. Manuals for some bench scopes with battery state that the scope should be connected to ground with a separate grounding wire when used with potentials above ~30 V RMS or so. Insulated BNC connectors are much more fragile, especially when mated with standard BNC hardware, so they're rarely used for grounded bench scopes.
Apart from this, I don't see any signal integrity issues, since the inductance of the long wire to the grounding rod is way too high to be of any use at typical oscilloscope frequencies. Keep in mind that even a 6" ground lead causes ringing with fast edges.