Hi,
From the autograd point of view, anything that you do (as long as it is differentiable) will be fine.
It then depends on your application what you want to do.
I guess the 3 options I can see are interpolate to scale up (or down) one to fit the size of the other. pad or crop. And replicate as you mentioned.
I think it will depend a lot on your application which one will work best so you want to test them and see how it goes.