As they say, "A bad workman blames his tools." It's really hard to say that they failed because of Microsoft tools. The fact is that they made bad decisions in how they would implement and use their tools. There's nothing to prove they wouldn't have done the same dumb things with open source tools.
Precisely. How many terrible, awful, untouchable projects are out there that run on top of a LAMP stack? wordpress.com comes to mind with their thousands of servers dedicated to basically caching. I strongly believe that a terrible hacker will manage to foul up even the most beautiful language/framework, while a good hacker will be able to write neat and beautiful code in even the most obtuse and awkward languages.
As for their actual infrastructure: not having a version control system and a build system (e.g.: never deploying directly from the VCS) is a must for any size team and sometimes even for single developers. Thankfully, nowadays most people do use VCS's but build and deploy systems are largely at the level of glorified shell scripts at best.
Exactly, a tool (technology-based or otherwise) is just a multiplier for the person wielding it. It's the people wielding the tool that make the difference.
Management is not excluded from this either. They have to:
1. know, in depth, the business they are in and the tools they use (or could use) to achieve their goals
2. listen to what their team tells them and provide an environment where they can do the job right
It sounds like there was a lot of micro-management and putting out fires in this case.