I'm not a frequent Blender user, but in all of the systems, the imported molecules match molecules that are exported from other molecular viewers (Pymol and Chimera, etc), so ePMV retains this default scale to match those systems for people who want to combine representations from different viewers. These come in huge in Maya and Blender and 3D Studio Max, but at a good size in Cinema 4D...
We strongly recommend that people never scale molecular data once it is brought in so you can update or alter the molecule in a future session, however, I realize what a pain it is to animate when things are 10 or 100x too big in the native scene. What I recommend is to build your model and modify it with ePMV until you are happy, then scale the parent object in multiples of 10, either make it 0.1 or 0.001 etc. Don't just use the manual drag to scale tools, do it to a perfect 10. That way, if you need to modify the molecule or make a new one for your scene or even bring one in from a different program, you can simply apply the same scale to that before you begin your scene design, rigging, and animation.
In the future, we should consider adding some sort of "Scale all data" button that will help make this process more seamless for Blender, Maya, and Max.