MeshFilter meshFilter = go.GetComponent<MeshFilter>();
Mesh mesh = meshFilter.mesh;
Vector2[] temp = mesh.uv;
mesh.uv = mesh.uv2;
mesh.uv2 = temp;

Note that this will cause a copy of the mesh to be created, and the engine will create a new VBO to put the data into.

Unfortunately this is less trivial than it sounds. It can be done in several ways, for example using a script that sets the mesh.uv to the mesh.uv2 set or using a custom shader that can switch between the meshes. An easier method, assuming you don't have a really weird mapping is instead of using 2 uv sets just use one and use texture positioning to switch to different parts of the texture. To give an example:

using UnityEngine;
using System.Collections;

public class UpdateTexture : MonoBehaviour {

    public Material background;

    void SetVerticalOffset(float verticalOffset) {
	Vector2 offset = new Vector2(0f, verticalOffset);
    	background.SetTextureOffset("_MainTex", offset);
    }
}