What workarounds are there for websites that block Safari Reader?
I have heard that readitlater works to assemble the full article whether you have paid for it or not.

I just went to the Introduction page in Safari 5.1 and reader is already to page 15. I'm not going to let it finish, but it doesn't look like it's blocked to me. I haven't paid yet - so something might be up in terms of server overload if reader isn't working for you.

The author of Instapaper did mention this specifically in his last podcast that it was quite possible technically for instapaper to scrape the whole article. The gist I recall is he didn't want to cross the line of bypassing ARS' intent since ARS has clearly decided to offer single page view as a benefit to their subscribers. 

He urged people to spend the $5 for a month's access if they wanted the whole article to load in instapaper for later reading.

My take is that many of the services actually made sure their tools would not parse the whole article out of respect for a journal as well as an author that penned 27,000 words.