You can definitely use FontAwesome with mojoPortal, I've done it in tons of skins. You need to follow the instructions for using the FontAwesome CDN here.

Then simply add your FontAwesome elements to the page. Example:
<i class="fa fa-flag"></i>

In the thread you mentioned I was talking to Audette about using FontAwesome for buttons/imgs generated by mojoPortal, I didn't mean to suggest that mojoPortal is incompatible with FontAwesome, you can definitely use them together by just changing your markup.

I have found loads of ways to get FontAwesome icons to generate where I want them through the theme.skin, but most of the time when you use them all you'll need to do is add the right markup to your layout.Master or your html content instances, depending on where you want it to show up.