The work of Germany in WWII was undone as much as was possible. Land was restored to it's respective owners. Country's governments were restored. Action was taken against germany to prevent such things from ever happening again. It was also acknoleged by the world as an atrocity. The German people look back on that time with shame and reference it as a terrible, dark time in their past.
Not so much as an apology has been made in the case of the celtic cultures. A good start would be allowing their independance when they ask for it. That's the very /least/ that could be done. And, you're right. Nothing will ever fix the damage.
Scotland is quite similar to ireland. The major difference is time. It wasn't nearly as recent but it was a LOT more bloody by comparison. Scotland has rebuilt while places like northern Ireland are still very affected. The reason for the religious involvement in Ireland is because the protestant church is associated with the, church of England (i.e. the invading military force.) Had the invasion never happened, the prejudice wouldn't exist. Remove the invasion and there's nothing to fuel that prejudice. As i'm sure you're aware, It has little to do with actual religious beliefs... It's just another way of identifying, "sides."
I believe that because Scotland has had a lot more time they're a lot more likely to be capible of standing on their own, and to not letting the past drive them to make brash, short-sighted choices. Maybe these are just the ranblings of an American who doesn't understand these situations as much as is needed to have an opinion, but i will applaud if Scotland gains independance through peaceful means.