Move object along waypoints, but affected by gravity

Hello,

I am trying to move an object along a series of waypoints, in a line. The typical solution is this:

 function Update() {
         transform.LookAt(targetGO.transform);
         var distance : float = speed * Time.deltaTime;
         var source : Vector3 = transform.position;
         var target : Vector3 = targetGO.transform.position;
         
         transform.position = Vector3.MoveTowards(source, target, distance);
         
         if(Vector3.Distance(source, target) < ARRIVE_DISTANCE)
             targetGO = pathManager.NextWaypoint(targetGO);
     }

This works great for moving from one waypoint to the next, however, it does not take into account gravity. For my scene, I am dynamically created waypoints along a path on the terrain. I would rather the character controller move towards each waypoint, but stay affixed to the ground (unless he's jumping). So the basic algorithm I'm thinking would be:

 -get next waypoint
 -if there is horizontal input, calculate movement towards next waypoint
 -after calculation, add gravity factor
 -move towards that target, and rotate towards it

What is the most effective solution to do this? Should I not be using MoveTowards, but instead do something like this:

     //somehow change moveDirection to take into account gravity?
     Vector3 moveDirection = new Vector3(Input.GetAxis("Horizontal"), 0, 0);
     moveDirection = transform.TransformDirection(moveDirection);
     moveDirection *= speed;
         
     //apply gravity
     moveDirection.y -= gravity * Time.deltaTime;
     Vector3 move = moveDirection * Time.deltaTime;

     controller.Move(move);

Any help is appreciated! Thanks, Ryan