Yes, certificates are still useful for Intranet SSL.
There's an important difference between SSH and SSL-without-a-certificate: when you first connect to a server with SSH, your SSH stores the server's fingerprint. If you then try to connect to what the SSH client believes to be the same machine but gets back a different fingerprint, it alerts you that there might be someone intercepting your communications.
SSL-without-a-certificate, on the other hand, does not store the server's fingerprint. Your communications will still be encrypted, but if someone somehow hijacks the DNS server as you mentioned, or, as Rushyo notes, does ARP poisoning or something similar, they would be able to perform a man-in-the-middle attack. SSH, as previously mentioned, would (supposing you had connected to the correct server some time in the past) notice that the fingerprint had changed and alert you.
A self-signed certificate would be comparable in security to SSH. A man in the middle could generate their own self-signed certificate, but as long as your applications are configured to only accept that self-signed certificate, you should get an alert similar to that that SSH will give you.
A local certificate authority gives you security similar to self-signed certificates, but may be more scalable. Should you have multiple servers, each can have their own certificate, but a client only needs the top-level one to trust all of them. If a server is compromised, you can revoke its certificate rather than having to change every server's certificate.
I don't believe an external certificate authority has any advantages, other than possibly less configuration if your machines already have the certificate authority trusted.
Lastly, I don't know enough about two-factor authentication to evaluate it, but for most applications, SSL should be sufficient.
Disclaimer: I am not a security expert.
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