1) As others have said xinput is pervasive as this point. If the Xbox 360 controller becomes hard to source then I'm sure a replacement xinput derived device will still be around. If not, it's a well documented standard and new devices can be made.
2) This leans on my first response. Xinput is the winner here, not the Xbox controller. If after testing they can't harden it then we have a lot of other options, up to and including a bespoke controller.
I guess what I'm saying is that video game controls are so much fun for a reason. They 'just work'. And while there is a little bit of dystopian sheen to seeing video games become the source for defacto tooling for war machines I'm always for a simplification of man/machine interactions.