You would have to edit a few things.
First of all, pick a building you want the unit to be built at in the proto (like, say, the Military Academy). I believe you'll see some sections called "Train" somewhere in it, with a number of units and techs (for example "Hoplite" and "Hypaspist"). Anyway, add another such section (a train unit one, not a tech) with new your unit name in the appropriate place... that is, the ProtoUnit name. Make sure to pick a button position (where the icon is placed in the menu) that doesn't conflict with another unit or tech. Also define a cost, civilization, and allowed age for your new unit.
There is also the option of making the unit automatically spawn when the player upgrades to Athena. Just look at some of the Atlantean Age-Up technologies. Which brings me to the second part; editing the techtree.xmb (techtreex.xmb with TT). Specifically the Age-Up technologies, even more specifically the Age 2 Athena technology. Go to the tech mentioned above and look at it. You'll notice that it makes units available to train (I can't remember the coding it has there off the top of my head)... for Athena there are units like the Hoplite and the Minotaur. Anyway, add another unit-availability thing (copy from the existing ones) and put your new ProtoUnit name in the field. Or, like I said above, you can make it spawn at a building automatically. The Atlanteans civs have this bonus... it makes the new myth unit for that age spawn at the temple. Copy whatever the format is for that, if you want.
Bada-bing, bada-boom. You can train you new, custom unit with Athena being worshipped. The same process applies to all such unit training. Let me know if you need something clarified.
Your Divine Overlord
KING JARED
Aw, hell, I dunno, she had some tig-ole-bitties, d'int she?
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