Can I get away with that poorly designed board?
Load caps should be between the MCU and resonator, otherwise they act as an antenna and might pick up extra noise, which, depending on the operational conditions, might mess with your timings.

I would suggest leaving resonator "horizontally" (space-wise seems to fit) and move load caps to the side of the MCU, between resonator and MCU itself.

In theory some older PTH resonators could be more thermally stable than SMD due to larger die, albeit suffer from some frequency deviations from nominal due to manufacturing tolerances.