I agree, a Franco-British Union would prevent Mers-el-Kebir happening. There are a few AH's where Reynaud doesn't capitulate/other members of the government agree with him, and the French Government moves to Algeria and continues the fight.
There are also a lot of AH's where Mers-el-Kebir still happens, but not as in OTL. Usually by Somerville going with Holland to negotiate, or by a different presentation of the demands to make the better options (for both sides) more palatable to the French Admiral