It is possible to setup TOR manually to work with a browser of your choice but it is a decidedly technical pursuit for many average users. (As an update, since the article says they don't like Windows, they apparently mean 'Use some version of TOR, just not the prepackaged TBB which includes Firefox.')

Regarding a 'standalone' version of TOR, they were likely referring to the Windows Expert Bundle. That said, I've never read anything to make me believe the Freedom Hosting takedown was due to the TBB. the NSA) who were doing that on any meaningful scale and current versions of the software purposefully try to keep up with security patches to minimize the amount of time a certain browser version might be vulnerable. However, it was likely only three-letter-agencies (e.g. In years past, the TOR browser bundle lacked certain security patches in Firefox that could have been exploited to uncover the identities of people using it. The admonishment to not use Windows if possible is a good one, but unless you are doing some really bad stuff, it is probably 'safe enough' (Linux is always preferable though). The TOR Browser Bundle (TBB) is safe in most instances. I would be skeptical of the article you read.

How to use tor browser on linux