I guess is an opportunistic encryption vs no-encryption scenario, since Snowden was sending his emails anonymously at that time there was no way for him to verify his identity to anyone. However, this was before there was any attention on him and sending his public key inside his first encrypted email would at least offer guarantees of the form: "If this connection is not MITM'ed now, it cannot become MITM'ed in the future". I suppose Snowden would know if there was indiscriminate and automatic mass-interception of GPG at the time (there might be now).
I am also not a crypto expert, but as I understand it: Micah could have also encrypted the email with the key given to him by the 'anonymous mailer', included the hash of that key as part of his message and then signed the whole message with his own key. Since Snowden trusted Micah's key, he could verify the email signature and then check that the included hash matched his own key. A MITM attacker could intercept Snowden's first email and change the key, but then Micah would have hashed the fake key and included that in his email, which the MITM couldn't alter without breaking the signature, then Snowden would have seen the wrong hash on the reply email and know of the presence of the attacker.
I am also not a crypto expert, but as I understand it: Micah could have also encrypted the email with the key given to him by the 'anonymous mailer', included the hash of that key as part of his message and then signed the whole message with his own key. Since Snowden trusted Micah's key, he could verify the email signature and then check that the included hash matched his own key. A MITM attacker could intercept Snowden's first email and change the key, but then Micah would have hashed the fake key and included that in his email, which the MITM couldn't alter without breaking the signature, then Snowden would have seen the wrong hash on the reply email and know of the presence of the attacker.