Well, I would not suggest removing the drivers/gles2 folder. Even if you are only wanting to compile with OpenGL-3/GLES3, removing the OpenGL-2/GLES2 folder is not really the way to go about it. Code that references GLES2 stuff is going to crash if the folder is missing. Instead, there should (hopefully) be a compiler option in Scons for building with just the version of OpenGL you want.
Based on the issue what I mentioned in my previous post, about libGLESv3.so, the issue is not GLES2 at all, but instead is GLES3. It seems the build chain cannot find the library for OpenGL 3, which is causing the issue. Unfortunately, it does not appear such an option is in Godot right now, but there still might be a way to build only using OpenGL 2. I would suggest asking the Godot developers on the devel IRC channel if it is possible to build Godot using only OpenGL 2 and see what they say. If it is possible, then that is what I would suggest doing.
(That said, if you can export your Godot project, not Godot source, to GLES2 in the Godot editor it may work on older versions of Android. It might be worth a try to open your project in the Godot editor, change the renderer to GLES2 in the project settings, export to Android, and see if the exported apk works)
