What do you mean by a "partitioned Mac Mini"? When you install Windows 7 using VMWare it does not involve creating a partition. The virtual copy of Windows 7 is actually one large file within OS X Yosemite. If you have in fact created another partition for something else, that's different.
And yes, just install Yosemite over itself and you won't lose data. However, you should make sure that you have a backup before doing so. Use Time Machine. Also, is there any specific reason you feel you need to do a fresh install of Yosemite? If you're having problems with something, a fresh install may not solve anything.