I really don't understand your justification.
One of the certificates literally has a private key of 4; it's as compromised as it could quite possibly be. This is not a "one of the intermediates have a weak and possibly crackable key" or "a bunch of incorrect certs were issued but the issuance was patched".
To a MITM attacker, git clones can be easily distinguished from visiting in Safari. You could choose to only poison git clones; without poisoning anything else.
Heck, you can probably build an exploit kit in a hour; camp out around a Starbucks or McDonalds with open wifi, and start compromising git clones and deliver malicious payloads.
An attacker absolutely cannot “easily distinguish” between a git clone and visiting the website and swap the certificate.
To know whether a request is a git client or web browser, an attacker needs to be able to inspect the contents of the web request (to check the user agent or whatever). If the site is using a legitimate certificate, the attacker has no way to inspect the contents because it is encrypted with a key they do not control.
If an attacker used their own, eMudhra-signed certificate, it would throw the certificate error in Safari.