Protected blocks of code work in Markdown Gists, and in fact your code is handled that way. If you check the blocks, you will see that they are contained in a div with class="highlight highlight-PHP" .
The problem is that PHP code is only recognized for GFM allocation if it contains a <?php delimiter. Add this to the beginning of each PHP block, and you should be fine, for example:
... ```php <?php class GO_Example_Model_Thing extends GO_Base_Db_ActiveRecord { ...
Chris
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