Context being everything, the French Navy was at that stage under the control of the Vichy government of France, essentially a German puppet government and had Churchill not attacked the fleet it was likely it would have been used against the British Forces.
It was likely that the French would've tried to scuttle the fleet had the Germans tried to requisition it, as happened 2 years later in Toulon [1]. But obviously, hindsight is 20/20, there was no way for the British to guarantee that this was going to happen.
I think "likely" is overstating it, given ultimately the Vichy government scuttled almost their entire fleet two years later when the German's tried to take control of it. (The German's in the end captured a small number of small vessels, all the technologically modern ones the German's were interested in—the much large destroyers and cruisers—were scuttled.)
That said, it may well have seemed likely at the time, and it's only from hindsight that this is clear.
The war was truly going badly for UK at the time, with US still not joining the war. And those French naval vessels HAD to be take out of the war somehow. The Royal Navy was mighty, but stretched very thin.
Had the French naval vessels been seized by the Germans somehow to be used in WW2 actively, it certainly would've meant Germans/Italians completely denying the UK ships from reaching Middle East via Mediterranean. This would effectively mean no more supply of oil, meaning UK would've lost the war.
The local French admiral had been warned to surrender/scuttle the ships but he refused on account of his honor.
[1]: https://en.wikipedia.org/wiki/Attack_on_Mers-el-K%C3%A9bir