Change output using a .jsx script for After Effects CS6
So, the answer to your question is 'yes, but...'

It's perfectly feasible, but you have to create an output module with the settings that you want, and then save it to your computer.  You can create this by going to Edit -> Templates -> Output Module.  Click on the 'New' button in the pop-up window, and then Edit it for the settings you need (quicktime, h.264, etc).  Save it as a useful name ("H264HighQuality" or something like that).  Save the output module, and you'll be able to access it from your scripts from there on out.

In order to use it in your script, just use:
app.project.renderQueue.items.add(myComp).applyTemplate("H264HighQuality");

As long as you've made the template first, you can access it in your scripts as many times as you want.  However, After Effects does NOT allow you to programmatically create Output Modules or alter them on the fly, unfortunately.  But you only need to make the template once -- as long as you have that template on the computer you're running the script, it should work just fine.