Adding fmath editor plugin to ckeditor through wysiwyg module
This started out as hacking it in, but things are always nicer in a module. The code is on my Github but if you just want the module it is hosted here for the moment. Full install instructions are similar to your link above and are including in the README for the module. 

Basically, if you have the Wysiwyg CKEditor module installed already, you'll need to:


Install fMath plugin:
Download the plugin for CKEditor from the fMath site
and unzip the package.
Copy the folder fmath_formula to sites/all/libraries/ckeditor/plugins folder
Install the fMath WYSIWIG module (linked above):

Download and add the module to Drupal and activate it.
Enable the fMath button in the WYSIWYG profiles page for the wanted formats (e.g. Full HTML).

Now, the button on toolbar should be displayed. When you click the editor, it should show up.
You will not be able to save the image to the page until you complete the next steps.
Install the server side script to generate the images:

Go to www.fmath.info/editor/ and download editorPhpServerSide-vx.x-x.zip
Unzip the file.
Create on your server a folder "capture", it must be available from www.yourserver/capture
Copy the file imageCapture.php to this folder, it must have the permission to execute.

Create a folder img in capture folder (capture/img).
Edit the file imageCapture.php and change www.yourserver.com with your server url

Edit the file sites/all/libraries/ckeditor/plugins/fmath_formula/dialogs/configMathMLEditor.xml
to add or edit the property "urlGenerateImage" to 
http://yourserver/capture/imageCapture.php
Test

Clear the cache of your browser (temporary files).
Create an equation and save.