The Problem with Saying "Biblical"

Today at the expense of the bold Sean Raybuck, we discovered the consequence of making reference to a religious text in the middle of a philosophy class.
Background: this is the Problem of Evil, which asks the question, “Is it reasonable to believe in an omniscient, omnipotent, and omni benevolent God (O3 God), in light of pointless/unjustifiable evil?” After two and a half days of lecture, we as students were able to begin what appears to be a semester long discussion. At one point Sean asked something to the effect of, “Where do we get the idea that it is an O3 God’s role to intervene when cases of evil arise, whether it is from a Biblical, historical, (and a couple more –cal) perspective?” (My apologies if I butchered what you actually said, Sean).
It seemed that the professor only addressed why we cannot refer to religious texts to solve the problem of evil, and made the case that God actually permitted/encouraged evil, using as evidence the flood in Genesis and the wars in which Israel was told by God to obliterate certain people groups. After a few minutes one student seemed to answer Sean’s question directly when he stated that it would be an O3 God’s duty to intervene in cases of evil. To be fair, the professor came around to pointing out instance in which God in the Bible did intervene in human affairs (parting of the Red Sea, the 10 Plagues, etc.). Sean and I talked after the class, and he said that this didn’t fully answer his question in relation to free will, and although God in certain cases did intervene, is that to be his typical role?
First I would like to respond to the professor’s claim that God of the Bible permitted/encouraged certain evils, such as the destruction of whole people groups. These “evils” were actually judgments, in which the people involved were guilty of their fate. With Sodom and Gomorrah, the people were so wicked that they would sexually assault any newcomers in the city. In other instances, the people groups were a warring people (such as those at Nineveh), conquering city after city, and exploiting those they defeated as best they could. So in essence, God was destroying evil, not perpetrating it.
As far as free will is concerned, I believe it is something that we as humans are given, but at the same time, I don’t know if we have the full ability to use it. The New Testament (since this isn’t philosophy class, I’m going to reference the BibleJ), describes non-Christians as being enslaved to sin, and even being blinded to what is good. It is also said that, “no one seeks to do good, not even one” (I apologize for the lack of references). In fact, Christ came to set us free from sin. So with this in mind, one could argue that we cannot do any good at all unless Christ comes into our lives and reveals to us what is good and gives us the strength to do that which is good. As a Christian, it is an interesting thought to realize that I probably need more grace than the non-believer, since I do know what is good and what is right and have the ability to choose, but still repeatedly decide to sin.

*As I was writing this, I realized there are a lot of ins and outs with the Problem of Evil that I’m not mentioning and which I may have to explain at a later date, or just discuss with you, my readers whenever we get the chance. Since my time is limited, I don’t really proof read these things, so I may have digressed from the main point. Leave me comments and let me know your own thought and opinions.