Hi Marin,
It's true that it's a pain to handle the encoding of h.264 outside of AE. You can write a script that calls the app.executeCommand() function and passes in the code that invokes the "Add to Adobe Media Encoder Queue..." found under AE's Composition menu. The correct, numerical, code for that command is 3800. So you would just iterate through the comps you wanted and then open them in the main viewer using the .openInView() method which brings them into focus so-to-speak. Once it's open you can then send the comp to AME with app.executeCommand(3800). On the AME side, you would have to make a default template for the render output settings you would want. When your script adds a comp to the AME queue it will take those settings.
Now, you could do all that, but have you seen AEmpeg that aescripts posted yesterday? It allows you to render to 100s of codecs using ffmpeg right from AE. While it costs some money, at least it will open up the door to a streamlined workflow and a variety of codecs that you might need.
--Arie