https://github.com/nodejs/node-eps/blob/master/002-es6-modul... was merged today; v8 C++ API for node to truly support it has not been implemented yet, should be in next LTS at current pace (next year).
Why can't node parse a file to detect if it's a module? The presence of a top-level import or export means it's a module. If it's not, then the parsed file can be kept if the file is also in strict mode. If it's sloppy, it'll have to be re-parsed. Seems like a small penalty if the goal is to enable migration.
Also, why worry about ES modules importing Common JS? Just disallow that and let projects migrate to ES modules bottom-up. Then you don't have to worry about executing a Common JS module to determine what its exports are or circular dependency problems.