Earlier quoted context omitted.
I know, but this does not make MD5 as broken as ROT13.
Depends on what you place in the expression broken. Md5 is useless in anything remotely related to security. An as a non secure function it is slow.
There are serious flaws with MD5, and I would never recommend its use today. But there is no known attack that can generate a malicious binary with an arbitrary hash. The attacker needs to control both files to generate collisions, which is a huge limitation.
Maybe those attacks will exist some day. But I wouldn't be setting fire to all your legacy software without first understanding exactly how they use MD5, and if that is vulnerable to any known attack.