I think whatever you do, someone is going to have the opinion that it is wrong and not in the piggies best interests.
For me, fleece is just too much hard work. So I stick with my megazorb/auboise/hay/newspaper combo which works well for me. I'm sure my piggies would probably be happier on fleece as it's more cosy but I can't justify it. I'm sure some people would "look down" on me for using that type of bedding but you can't please everyone.
For people who use fleece, I think you should just go with it. Although the article is very interesting and has some valid points, at the end of the day we do live in a cotton wool society and unless you had a genuine issue with fungal infections etc a few germs aren't going to do piggies any harm. The same as how, a few germs don't do babies or humans any harm either.
I've been picking up guinea pig poo and forgetting to wash my hands for years now and I'm still alive 
|)