Let thy chief terror be of thine own soul:
There, 'mid the throng of hurrying desires
That trample on the dead to seize their spoil,
Lurks vengeance, footless, irresistible
As exhalations laden with slow death,
And o'er the fairest troop of captured joys
Breathes pallid pestilence.
We have to admit, we had to stop and think about this one, too, so don't worry if you were a little bit puzzled about it. Let's break it down a little bit: the speaker is commanding the reader (us) to fear nothing so much as we fear our own souls. How come? Well, the speaker seems to be saying that, if we go rushing after the things we want without thinking about how we affect others, our souls will punish us and we won't be able to enjoy our gains.
OK, so what does that mean in Daniel Deronda? Well, the first person who comes to mind is Gwendolen, who prioritizes her own gains at the expense of others. She can't enjoy her comfortable new life when she marries Grandcourt because she knows that she has hurt other people on her climb upwards, and as a result she feels totally tormented. But beyond Gwendolen's experiences, we can't help but think of other characters like Daniel and Mirah who are also greatly troubled when they look within themselves. Maybe George Eliot meant for this epigraph to serve as a warning to the reader: try to be careful when you look too deeply within (yourself, the book, etc.), because in this book you're going to see that learning the truth about yourself can sometimes be a scary but eye-opening experience.