I am designing a board but space is not a luxury that I have at the moment, can I get away with that design or I must use a SMD resonator?
You could "Get away" with a design like this. A good clock design keeps the traces as short as possible, and the capacitors and traces symmetrical to keep the parasitics equal. A copper pour can also be a good idea on the top layer around the components to increase capacitance to ground, and shunt high frequency signals to ground.
The biggest problem with crystals is radiated emissions, and depending on the country your in this could be a problem. It's best to use good clock design practices to avoid problems.
One thing you might be able to do is mount the crystal on the other side of the board to decrease spacing.
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.
It depends on what you mean by getting away with it. There are a few considerations:
1) Your Xin and Xout traces are of different lengths. It looks like the difference is small enough not to be an issue, but without knowing more about your application, I don't know.
2) If it's an HC49-U, it will really loom over your chip and make it hard to probe. If HC49-S, it won't get in the way quite so much.
3) If you decide to switch to SMD, keep in mind that they have very different -R and pullability than HC49 (they will be worse than HC49-S, which in turn is worse than HC49-S).