So, like many of you, I was disappointed to find that we didn't have and most likely wouldn't be receiving a new trainer option for the Hammerhead.
After playing with it a bit, I discovered that the only place that it would really be useful is the 2nd mission, where you have to collect the artifacts. Here's how you beat it.
First off, the Hammerhead can't take much damage. That being said, it can target and fire at ranges longer than the opponents you'll be facing can engage. So, your best option here is to enable the Easy Kills option, and just fire before they can fire at you. Remember that the missiles target, and aren't line of fire, so you can fire them from weird angles and be fine. The only problem with this is that if you take a single shot, you're toast. Also, hiding helps, especially with the last grouping of Geth. Eliminate them quickly, and you'll be fine.
Hope that helps!