The author of the article says:

"The whole mentality here is that anybody can change the source of a project, submit it, and you never know what kind of compiled binary you're going to get."

Not if you can prove to your superiors that the source code you want to use is managed and moderated by code maintainers in order to review the code prior to it being submitted into a code branch...

... and that your superiors have a policy of only obtaining code from said moderators and code maintainers at officially announced places of acquisition of stable code branches.

This covers many popular free and open-source software from many organisations such as the Free Software Foundation, Mozilla, the Linux Kernel Organisation, and others, whereby the contributor base is large enough for the code to be peer-reviewed and managed in ways that will prevent such malicious attempts at code pollution from ever becoming a reality. If you can show that the project belongs to an organisation that honours its reputation for the production of quality software, then it would make the rejection of the use of such software due to this argument much more difficult to justify.

While this doesn't cover every free or open-source project under the sun, it does cover many of the more popular major projects where a Windows build is available or supported.

--tonza