I am currently using the following function, but it does not seem efficient enough, so i am also looking for a better solution.

// Load specified texture and only that texture in given terrain
void LoadTerrain(TerrainData terrain_data, int texture_level) {

    float[, ,] alphas = terrain_data.GetAlphamaps(0, 0, terrain_data.alphamapWidth, terrain_data.alphamapHeight);

    // make sure every grid on the terrain is modified
    for (int i = 0; i < terrain_data.alphamapWidth; i++) {
       for (int j = 0; j < terrain_data.alphamapHeight; j++) {

         // make sure only set layer is visible
         for (int k = 0; k < terrain_data.alphamapLayers; k++) {
          if (k == texture_level) {
              alphas[i, j, k] = 1;
          } else {
              alphas[i, j, k] = 0;
          }
         }
       }
    }

    // apply the new alpha
    terrain_data.SetAlphamaps(0, 0, alphas);
}

http://answers.unity3d.com/questions/285816/change-terrain-texture-and-tree-at-runtime.html#answer-285924

a little upgraded script that allows to change texture without full repainting, e.g. it saves paint map and changes texture.