Apparently Konami did a rather clever way of doing what the Japanese text did, sort of.
The first section is essentially the same as the Japanese.
Unhandled exception at 0x1i-666 in qliphort.exe: Access violation writing location 0x00-000
Ignore the error and continue? <Y/N> …[ ]
The second section however is an Atbash Cipher in Spanish:
Cipher: Hv kilsryv vo xlmgzxgl xlm vo Ziylo Hztizwl. Vo Uoztvol sz hrwl oryvizwl.
Spanish: Se prohibe el contacto con el Arbol Sagrado. el Flagelo ha sido liberado.
English: Contact with the Sacred Tree is forbidden. The Scourge has been unleashed.
Basically it covers both parts of the original message:
Behold, the man has become like one of us in knowing good and evil. Now, lest he reach out his hands and take also of the tree of life and eat, and live forever.
God is angry on your doing and want to bring Fire Flood.
You know, in a non religious manner. Since religious issues.