Personally I am much more upset by the fact that many manufacturers are moving to flat mount disc brakes (that are limited to 160mm) rather than to discs per se which is a welcome change in my opinion. If nothing else for the decoupling of the breaking and rolling elements.
When it comes to thru axles I have a mixed opinion. It just so happens that I plan on replacing most of my bikes in the next years, in all cases going for models with discs and TA. This will allow for them to share wheelsets between them, which is a pro. On the other hand for things like dynamos or internal-geared hubs the choice is not yet on par with QR options. There are maybe three TA dynamos I can think of, and in all cases they are more expensive than the QR equivalent from the same manufacturer. Also, the hypothetical increase in stiffness of a thru axle is likely negligible once you factor in the whole bike/wheels as a system.