No contest: taking Beaune as the destination, GVA is 144 miles away on mostly low traffic highways, CDG 208 miles including the stressful Paris bypass. GVA is a small, easy to navigate airport. The border is often unmanned, with most non-suspicious vehicles waved through when staffed.
If Burgundy-bound do book your rental car for pickup on the French side of the airport, which will yield lower rates and less conspicuous local plates.
The one drawback is that a CHF40 Swiss highway sticker is required for the short stretch between GVA and the border, and a French rental car will most likely not have it, unless a previous renter invested into one (odds are better in the fall than early in the year).
If so motivated you can circumvent this by taking the D884/D1206 roads between Geneva and Bellegarde, where you can hop back onto the A40 highway.
Orly these days caters to domestic and leisure destinations, mostly on charter/low-cost/developing countries carriers.