How do I make node_gallery image thumbnails retain original proportions?
Never used this module, but try checking /admin/config/media/image-styles perhaps the module has an image style. If so, all you have to do is edit it and change it to your liking.

Side Note: You can also get there by clicking configuration, then under media click on Image Styles. 

As you wrote in a comment:


  Editing the node_gallery_thumbnail style to replace the "Scale and crop" effect with a "Scale" with the same numbers for width and height did the trick.