There is currently no way to tell Filebeat to ignore the HTTPS_PROXY or HTTP_PROXY environmental variables aside from relying on another environment variable, the NO_PROXY variable. In Windows environments this is particular difficulty because:

The service control manager does not support passing custom environment variables to a service at startup. Also, the service control manager does not detect and pass on changes to environment variables as the service is running.

Filebeat should support a configuration option of its own for this purpose.