Deleting the Win 7 boot in System Config will not have any effect on any of the data on your D:/ drive.
Deleting the Windows directory and both of the program files folders from D:/ will not cause any issues as Windows 10 would be on the c:/ to confirm this you can paste “%windir%” (without quotes) in a run dialogue box (winkey + r) or any file explorer to confirm where Windows 10 is running from.

Before proceeding I would still be sure to have a full backup of your Hard Disk Drive.

Let us know how it goes, if you have any issues deleting any of those directories you might want to take a look at this neat registry hack to provide a take ownership options in the right click sub context menu. You would not have to follow every step, you can also use the .reg files in the URL at the bottom of the article.