Naah, a 43mm diameter circular sensor would be perfect...no wasted image circle or sensor area. What about production cost? No waste there, either...after all, they can just ball up the excess silicon wafer and roll it out for another round of cutting, just like cookie dough. Mmmmm...wafers and cookies, I need a snack!
I see you needed to get in your quota of snark today.
Waste? Sure, allowing some of the silicon to go unused is certainly waste, there's no doubt about that. But then, for all of us who don't make a living out of it, it's all waste. Every camera that sits unused is wasted. Waste is particularly common for all those who get new e-toys (e.g. smart phones) frequently, either due to upgrade envy or through negligent loss/damage. Losing some silicon to a (relative) minority of pros and serious amateurs certainly requires a cost-benefit calculation. However, we're looking at 3-5 years (pulling numbers out of the aether) before pro-grade mirrorless becomes dominant; in that time, the costs associated with the wasted silicon almost certainly will have diminished.
And waste is already occurring in DSLR's: consider those who crop almost every shot (e.g. birders); they are also wasting silicon because a large fraction of their pixels rarely contribute to the final image.
So yes, there will be waste; the only question is whether it's worth the benefit of a larger sensor area, without having to replace all of your glass.