All right, I think I found a solution. Of course it's not an elegant one, but at least it works flawlessly on any situation and avoid any kind of coupling (if this is a right term) between my theme and the plugin.
The problems is that, by using
get_the_content(), WordPress does not apply any filters to it. It only does it using
the_content(). So, what we are going to do is use it.
As we know the_content prints on screen but, what happens if we put this onto a temporary buffer? PHP function
ob_start() creates an output buffer, which will held the contents without displaying them, and those contacts will be affected by the filters for sure. Finally, we will call
ob_get_clen() to retrieve and store them in a variable and clean the buffer. Pretty neat. Here's all together:
// Whatever you have to do here...loop, etc.
$theOutput = ob_get_clean();
// ...whatever you have to do with the output, now with all filters applied (and, on this case, with lightbox working flawlessly