Duncan was silent, for he was also at a loss as to what he should do. If Jacob really achieved a breakthrough, no one would be able to say for sure who would survive.
What was most important was Jacob and Mr. Santoro's relationship. When Jacob was in the South, he could still hunt down the former. However, Jacob's return to Hillsborough meant that he was back under Mr. Santoro's protection.
If he really challenged Jacob and was close to defeat, he could not be certain as to whether or not Mr. Santoro would save Jacob.
That was something that no one could be certain about.
Jacob had caused a scene at the Nixon residence and was attacked by the people in it. Just as they were about to kill him, Mr. Santoro appeared.
Evidently, Mr. Santoro did not want Jacob to die.
Hence, Duncan was trapped between a rock and a hard place—he did not know if he should fight against Jacob or not.