While I agree to OP, it feels not very thought-through, I guess it is how the mission selection works. Since certain missions are dependent of the state the target system is in, if you could "pause" a mission you could have outcomes that`d increase a state which isn`t active anymore. It is not a good reason, but the only viable I can think of, since the missions seem to be generated per-client and not from a server-wide pool.