Always worth looking at the french SIA CIVILE website, as they have a good NOTAM section (not just for France) and a good chart showing the activity of the military low fly corridors (AZBA Charts - a picture speaks a thousand words). Plus it is all free and available in English.
You can also access the AIP and print out any aerodrome charts you might need for the flight if you dont have them.
The lowest point of the Jura is to the north, around the area where La Paz DME used to be. That will bring you out at the north end of Lac Geneve. Just beware of the Nuclear power station / ZITs to the south west of Geneva if you get forced that way due to weather, as busting those will mean the French authorities will bust you, and poss your licence. You are correct about the controlled airspace heights / altitudes. Basically stops you needing to low fly to remain clear of the airspace above. Geneva Info are really helpful, although you may need to telephone the local BRIA(french) to close your flight plan (if you have one and have landed in France) and landing off airfield.