I would not say I believe that God “cannot miraculously intervene every time someone decides to do evil because that is not truly free will.” That said, as a theist obviously I believe God allows suffering. The question becomes why does he.
I think it is a good question. I also think we will not know the entire answer until our next stage in life (after this physical body, when we're in the spirit). However, allow me to explain that a bit so it isn't a complete cop-out.
It seems to me that this physical life in this universe we currently reside in, is one enormous birthing and testing ground for spirits. While it is certainly a beautiful celebration of creative power, it is also largely a test to determine who will develop enough love, patience, and self-control to be one with God.
Have you ever tried raising a person from infant to adulthood? Every child has been wrong many times about what they "need" or "require" for long term health and growth. In fact, rarely can kids tell you what they need to do to grow in a healthy, smart way. They're just kids. Sometimes parents must allow the child to learn from suffering, at times, even when it hurts to watch. Often the developing child can't comprehend why that happens, and even view loving parents as terrible terrorists sometimes. At the least, all kids will wonder at times why their parents work or make them work and don't just "live the easy way" (or what they think is the easy way).
I say all that because if we indeed are the equivalent of spiritual embryos, and if God is trying to grow us toward divinity, then we too are "just kids" in a sense. If the examples we see before us in our own physical development and growth show us what to expect when a spiritual God father's us, then we should expect to be left wondering, hurting, and confused sometimes. However, we are actually deeply cherished, God is sorry that we have to suffer like this, God suffers Himself with us, and this has to happen for our growth (in the eternal, spiritual perspective) and eventual good.