I have a friend who quit teaching because he doesn't like dealing with difficult students in the classroom. He said, "I just want want to come to work, to teach, and come home." Then I said, "Then, you really don't want to teach." Having difficult students in a classroom is part of teaching.
Likewise in running, I hear people say that they used to run but quit because their knees hurt too much. But I say that feeling pain is part of running. When a new stress is exerted, your body fires up the pain sensor in your brain. But your body also actually adapts to the stress, eventually, making you able to withstand the activity.
To improve in running, be ready for pain. Pray not to take away the pain, but pray for strength to get through the pain. Here is a Bible verse, suggested by a runner friend of mine, "I can do all things through Christ who strengthens me." (Phil 4:13). When pain sets in or the run gets really hard, repeat and ponder on the verse as you keep going. Praying through pain does not only improve your running, it also strengthens you spiritually.
Life has its impending difficulties, too. We face them, feel the pain and hardship, and eventually get through them. Then we find ourselves stronger than before. Let's take it from Bruce Lee, a Legend in Martial Arts, who said, "Do not pray for an easy life; pray for the strength to endure a difficult one."
P.S. My caveat: Please distinguish good pain from bad pain. What I wrote above is the good kind of pain. Bad pain? Please see a health professional.