You're overthinking this one, I think. The issue here is that, if you enter France from Switzerland there is no passport control and thus no one to stamp your passport - visa or no visa.
On arrival in Switzerland, you should point out to the immigration person the fact that you have a long-stay visa for France, but that you are simply arriving via Switzerland. Let them decide how they want to handle it, but trust me, you are far from the first person to do something like this.
Either they will stamp your French visa - OR, they may stamp your passport with the "usual" Schengen tourist visa stamp but on the same page or in proximity to your French visa. If asked to provide a photocopy of your visa with entry stamp, just make sure you get a picture of whatever stamp the Swiss put into your passport on arrival. That IS your entry stamp for visa purposes. If you have OFII papers with you, you should show those to the Swiss Immigration official, too. He may or may not need/want to stamp those.
It shouldn't be a big deal either way, but just make sure that the Immigration guy in Switzerland is made aware that you have a visa for France.