Great question! The short answer is no, ML is not still needed to capture decent audio in the Canon 5D2. Although certain Magic Lantern functions (such as zebra bars) are not available with stock Canon firmware, the primary advantage of Magic Lantern was that it allowed for manual control of the record levels in the camera. This avoided the fluctuating volume caused by the lousy Automatic Gain Control circuits in the camera. The ability to set manual audio levels has indeed been added to the Canon 5D2 firmware.HOWEVER, the audio circuitry in the 5D2 is still very poor. Anytime you record in-camera, you’re going to have more hiss or noise in the recording than you would if you did dual-system sound. The best workaround is to use an external preamp (an on-board one, like the Juicedlink CX231, or a standalone one like the Azden FMX-42. The less the camera has to amplify the signal, the better it will sound. Moreover, both of these devices provide phantom power, which is required to power many professional microphones.
Here are links to the two products I mentioned. I have purchased and used both of them, and they are excellent.
The heart of an audio system for professional video production is the field mixer. Generally speaking, the more expensive the mixer, the less noise (hum/hiss/etc.) it introduces to the signal it’s amplifying. This Azden mixer is an outstanding value, because it is much quieter than any other mixer (that I’m aware of) within $500 of its price.
Sometimes, you’re running and gunning, and don’t have the luxury of a separate field mixer. But, if you still want good audio, you need a separate preamp. The Juicedlink fits the bill. It has superb, quiet amplification, mounts directly to the bottom of your camera, and provides phantom power.