"But behold he doth not command us that we shall subject ourselves to our enemies, but that we should put our trust in him, and he will deliver us."
Pahoran is referring to very literal enemies who are trying to take over the government and destroy the freedom of the people. Together Captain Moroni and Pahoran are able to withstand the king-men and restore the government to the chief judge. The Lord, and His power, was with them, allowing them to be delivered from their enemies.
In applying this scripture to our own lives, we should remember that our enemies don't always come in the form of people that hate us. Enemies, in gospel terms, are things that try to pull us away from the Iron Rod and lead us down the wrong path. We should also look closely at the word "subject." If someone were suffering from a debilitating illness, something that threatened their faith so that every day was a struggle to keep going onward and remember the eternal purposes of life, that illness could qualify as an enemy. This particular enemy also counts as a trial, something the Lord has given this person to help build their faith and testimony. In this case, not allowing ourselves to become subject to our enemies takes on a little bit of a different meaning.
Here it doesn't mean that we won't experience trials, but that we shouldn't allow ourselves to be ruled by them. The person who yields to the enemy of illness allows himself to become bitter and resentful that he has to suffer rather than seeking the Lord's will and allowing himself to grow from the experience. The same thing applies to the enemies known as death, pain, sorrow, etc. When we face each of these, or any other "enemies," we should remember Pahoran's counsel to Moroni and "put our trust in [the Lord], and he will deliver us." Keep in mind, of course, that the deliverance is on the Lord's timetable and not ours.