(They think that the Confederates have not yet withdrawn;) and that they are still close by and will return.
(and if the Confederates should come, they would wish they were in the deserts among the bedouins, seeking news about you;) means, `if the Confederates should come back, they hope that they will not be present with you in Al-Madinah, but that they will be in the desert, asking about news of you and what happened to you with your enemy.'
(and if they were to be among you, they would not fight but little.) means, `if they are among you, they will not fight alongside you very much,' because they are so cowardly and weak, and have so little faith, but Allah knows best about them.