I believe that God is indeed omniscient. You have to recall that we are mortal beings, and our mind are finite. There is only so much that human beings can understand, the fact that we are God's crowning achievement notwithstanding. We are fairly intelligent- at least some of us are, in any event- but some things transcend the limits of human comprehension.
One possibility is that God has access to knowledge of the future. Think of it like a metal office cabinet. He can look there at any moment and see what the outcome of any event will be. What if, for the sake of argument, God chooses not to see it?
I subscribe to the free will hypothesis. Ergo, I believe that we are in control of our lives, and we make decisions of our own volition. For example, it is a choice to believe in God or reject God. Being that we have free will, it may be that the future, at least in terms of the outcome of human affairs, may not be set in stone. Perhaps the future is being altered at every moment through complex choices. Perhaps human beings are capricious by nature, and our choices cannot be determined in advance. Human decisions are often complex, although they can sometimes be somewhat predictable. Rationality and logic do not always triumph, and we often make decisions predicated upon emotion. Perhaps the future is nebulous, at least in terms of human free agency. You know that, for example, the road in front of your house can take you to town. But is that the only means to get to town? There are other routes you may take, but still end up at your destination. So in this regard, I believe that God can indeed prophesy about future events. Perhaps some things are inevitable. It is a moot argument to try and imagine what God thinks. I certainly cannot do it. I doubt even gifted men like Stephen Hawking can, either. We are not gods.
I think that you are connecting God's omniscience with the nullification of free will. But I have yet to see anyone demonstrate precisely how God's knowledge would interfere with choices we make. Perhaps God knows how we will choose, but it has no bearing on the choice. The accord still belongs to the sovereign individual.
Think of this analogy. God is probably in a higher realm of dimensionality. He can see time in a different fashion than we can see it. He can see the entire past and future at his own leisure. We experience some sort of temporal linear reality, and since we are trapped in three physical dimensions, we cannot extricate ourselves to the vantage point of God. Like a video cassette, God has the capability to rewind or fast forward the tape, and he can see the ramifications of future events. Be that as it may, his capability has no connection at all to human volition. God has the privilege of seeing what will be (or perhaps what MAY be), but our free agency remains very much intact.