I haven't used RM2k3 for a very long time. I suppose the first thing you would need to be able to do is track which members are in the party at any given time. To do this, you could reserve four variables, whenever you add an actor, you would set the next variable so you track where each actor is in the party. Whenever you remove them, you take them out and bump up the others. That way, you will have variables that always tell you who is in the party.
Then, when it comes to the summon skill, you could maybe attach it to a common event which would remove all the party members and add the summon (I don't remember if this can actually be done by default in 2k3; you might need to do it by having a page in every battle which checks if any of the summon skills have been cast by other methods (maybe you could make a dummy state and inflict the user whenever the skill is cast and just check if the state is on him)). Once it is killed, you would then add the party members back in order using the variables which track them. However, you would need to find a way to make it so that it doesn't go right to gameover when the summon dies; there might be a way, but I literally haven't used 2k3 for nearly a decade and when I did, I totally sucked.