I've long since moved over to a Mac, but also found ADigitalMan's guide extremely helpful back in the day.

I'm not sure what the current best way is on Windows to rip a BluRay, and then convert the M2TS files into a suitable format. But doing a google search along the lines of the above should yield some results. You may find guides on FanEdit.org.

If you rip the audio on a BluRay to an AC3 using whatever method you find, you can follow ADigitalMan's guide for that at least to separate it into 6 discrete channels.

Perhaps the most important question here is....what's the fun of a "clean" version of Game of Thrones?! ;)