Yep, they did not have though hole version, so they improvised. Now, flat pins provide more rigidity compared to round ones (at least in one direction).
At the same time, in my experience when you do this, metal weakens that you can realistically only un-bend them one time, after that they just break.
If you are bothered by it, find a crystal with the same frequency and replace it.
And it is strange that they even bothered to remove the plastic part. It is possible that they got the crystals from production line before the plastic was applied. Possibly even scraps that did not pass the test. Look under the package where the pins are attached. Are there any signs of bending?