I do a couple of different things, depending on the book and how I feeling at the time.
If the calibre ToC generation adds the id to the heading, I will frequently change the existing heading to a paragraph and add a heading with a class to not display it at the top of the file. This usually happens when there is a bit of code at the start of the chapter to display an image or something.
Other times, I generate the ToC, open the NCX and remove the anchors with a search for:
and replace with the double quote.
Of course, this doesn't work if there are headings elsewhere in the chapters.