Wolfire is separate from the Humble Bundle (Aubrey and I have no stake in it), and I don't have any inside knowledge about how the THQ bundle happened. However, I do support their decision to run it. Here are the pros and cons as I see it.
Helps people with less money afford a bunch of big games for the holidays
Helps fund the Humble Store and other indie services
Expands the audience for future indie bundles
Could help THQ out of a rough spot
Helps prove that pay-what-you-want can work with big-budget games
This particular bundle is Windows-only and has Steam DRM
It would have been ideal to get all the games ported to Mac and Linux and DRM-free, but there are major technical obstacles: these games use dozens of large Windows-only middleware packages, and were created with Steam integration in mind, so making a non-Steam Linux version of every single game would be a long and expensive process. This is why Overgrowth uses no closed-source middleware -- it makes it almost impossible to port to new platforms. It becomes more of a biz-dev problem than a technical one. You have to convince every single middleware developer to port it themselves, or give you source code access so you can do it in-house.
Also, this bundle doesn't replace any indie bundle, it is purely an addition to the bundle schedule. If there were no THQ bundle, there would be no extra money for charity, no major mainstream news event, no exciting new experiment. Given that it was impossible to get the THQ bundle cross-platform and DRM-free, should Humble Bundle have just dropped it and walked away? "Sorry, THQ. Sorry, Red Cross. Sorry, sick children, Sorry, poor gamers. We just can't budge on the Linux thing."
I'm sure it was a hard decision to make an exception to two of the founding principles of the bundle, and alienate some of the original bundle supporters, but it would have been a mistake to pass up such an important opportunity.
What do you think would be a better way to handle bundles like this in the future? Should they always have an ultimatum of Linux and DRM-free or nothing, or is there some middle ground for quality games that can't be ported?