It is probably better to examine this quote by also including a bit of the quote that comes before it and after it. Just before the quote in question, Santiago sees the star Rigel and knows that all of his "distant friends" would then be out.
He then says the quote in question and follows it up with some thoughts about the natural order of the world as it relates to predator and prey relationships. He then admits that he doesn't understand it all and reiterates the fact that he is glad to not kill the sun, moon, or stars.
I do not understand these things, he thought. But it is good that we do not have to try to kill the sun or the moon or the stars. It is enough to live on the sea and kill our true brothers.
Santiago has great respect for the natural world because he understands that he will live and die by that natural world. Despite this seemingly kill-or-be-killed attitude, Santiago considers the fish, the stars, etc. his friends. It is not a physically easy or emotionally easy thing for him to take the life of something in nature. He knows that he must do it, but he doesn't necessarily take pleasure in it. Santiago also understands his limitations within that natural world. He knows that his struggle with the fish is just about at the outer edges of his capability, and he accepts that limitation. It shows his humility and his knowledge about his place in the world. That's why he's glad he doesn't have to kill the stars. He knows that it is beyond his personal ability, and Santiago is okay with that.