Spent a month in Font last October in my van and had very similar worries to yourself. Unfortunately as was said earlier there isn't really anywhere "safe" and for me it was mostly about using common sense.
I generally only parked up at an area if there were already quite a few vehicles there already. This meant that in the middle of the week I climbed at Cuvier as generally there were lots of cars, lots of people and quite often the guy selling stuff from his van. I would definitely echo the advice of not parking on the other side of the road as it is much lonelier over there. Roche aux Sabots/ Cul de chien car park was also generally okay and busy even middle of the week. Elephant at the weekend was fine but I went once mid-week and really didn't fancy leaving my van there as it was completely deserted. Buthiers seemed okay as there were quite a lot of people but can't remember if that was at the weekend.
All in all I was completely paranoid about being broken into (as I had all my gear in the van) and really limited myself to only busy areas and was happy to not go to areas with stellar lines but lonely car parks! I have been before using a car and formula 1 hotel approach and that time we just emptied the car completely, left the glove box open and the parcel shelf off the boot and was pretty happy to go anywhere.
Anyway, all that said I think a lot of it is down to luck and whether the thieves are out that day. Obviously a bit of common sense helps reduce the odds.
Hope some of that helps, I make no claims to be a Font affionado, really just a summary of how a very paranoid van driver managed his time there.
Have a good trip
Dave