Modifying Material.sharedMaterial will change the .mat file. Add this script to any object you don't want this to happen to.

SharedMaterialReinstantiater.cs

using UnityEngine;
using System.Collections;
using Vexe.Runtime.Extensions;
using MaterialCache = System.Collections.Generic.Dictionary<UnityEngine.Material, UnityEngine.Material>;

public class SharedMaterialReinstantiater : MonoBehaviour {

  private static readonly MaterialCache _cache = new MaterialCache();

  void Awake() {
    var renderer1 = GetComponent<Renderer>();
    Material cachedMat;
    if (!_cache.TryGetValue(renderer1.sharedMaterial, out cachedMat)) {
      cachedMat = new Material(renderer1.sharedMaterial);
      Debug.Log("Found new material " + renderer1.sharedMaterial.name);
      _cache.Add(renderer1.sharedMaterial, cachedMat);
    }
    renderer1.sharedMaterial = cachedMat;
  }

}