Upon interating on a solution, I found two approaches:
1 : Create a custom importer for a custom format, so we would rename the .pngs to .XYZ extension, godot will not import them, then on Godot we create a import plugin to read that as what we wanted specifically, a atlas texture from the image files in the folder.
2 : Create another empty project just to handle this, so we can let it importing in the background while working on the main project, once it finishes, we set in the empty project to import all the thousand pngs to atlas texture, then after that, move those resources to the main godot project, this way it imports as we wanted, and it only takes some seconds to import the atlas and read the files, because .import files are present telling it is part of a atlas texture, godot will not import the pngs as individual textures, which is the expected behavior.
Option 2 is now my workaround for this specific issue, I guess the main problem is the editor freezes everytime is importing something.