No, I wouldn't call instinct a memory, but I really think you're focusing on the wrong thing here.
The relevant distinction here is not how "completely and directly" something is "explained by physical attributes"; to be honest, I'm not even really sure what that means. All behavior comes down to physical phenomena, after all; whether or not we can currently make that reduction explicitly is more a property of our current state of knowledge, than a property of the physical system itself.
The relevant distinction here is the fact that this behavior, like a memory proper, was acquired during the mouse's lifetime, not inherited, and yet passed on to offspring anyway. And yes, as you've noted, instances of that had already been observed -- this wasn't something revolutionary -- but still this wasn't a case where people expected to see that.