That usually happens to rogue characters. I have noticed that my disposition goes "eevil" when I order my thugs (from residence), thieves etc. to do crimes (pickpocketing, killing etc.). I still have no idea how disposition affects anything as I've managed to get up to the ranks of Supreme Commander and then when I killed Queen I was crowned as King (when I went for Sovereing and Supreme Commander, then everyone voted for me regardless of my disposition).
Just detirmines how the next generation will think of you. Religous level decides if you are immune to inquisitors or not (You cannot be tried as a "Fanatic" for an Inquisition which adds one level of severity to the trial) --- "I kill people like you on the way to real problems. Although in 30 minutes, the galaxy is at stake and you should fix the problem yourself" Shepard