I had to run around the internet for a little while to figure this out, and no concrete solution was available for Microsoft Office 2010. So, I did a little snooping around the Word 2010 Options and found out how to stop “Do you also want to save changes to the document template” dialogue box from appearing every time you save a .doc or .docx document.

I am assuming that somewhere some group of hard-working people care for that option to popup, I am not one of them. I find it utterly annoying.
Long story short, here’s the fix.
Step 0: Open the Word Document that keeps giving you “Do you also want to save changes to the document template” dialogue box when you try to save it.
Step 1: Now go to File > Options > Add-Ins

Step 2: Select Templates form the “Manage” drop-down menu, and click Go…

Step 3: In the “Templates” tab, erase whatever is in the “Document template” text box, and click OK. If Word prompts you to save the original template, choose No.

That’s it!
Now try modifying the document and saving it. The annoying popup asking to save changes to document template should be gone.
Hope that helps. If you have a better way to accomplish this, post it in the comments.
WARNING: Do keep in mind that you are dissociating the template itself from the document. This means if you want to change the original template, you won’t be able to do it from the Word document. You’ll have to go to the original .dot or .dotx file and modify that.