I am in the same situation because of some weird school redistricting that sent my children to middle school far away (and via a toll road, to add insult). We picked a place walking distance to the elementary and not far from the nearest middle school, but they redrew lines and sent children in our neighborhood to a much farther away middle school. I briefly considered moving, but it is in the opposite direction from my work and it would end up costing me in housing, gas, and road tolls to work since I don't pay gas for the school bus.
In your situation, moving sounds reasonable. Could you move part way there and reduce the commute to work, shorten the bus ride, and still not be quite in the city?