I have the exact same issue.
The "Workspace Cleanup Plugin" works ok - not following symlinks - at version 0.16 though.

Same issue occurs when using 'Wipe Out Workspace' so more of a core issue than git I think.

Workaround is to use directory symbolic links (mklink /d) rather than junction points (mklink /j).

It doesn't help that the Java runtime (maybe assisted by Windows) claims that junction points are a directory.

Create a new freestyle project named JENKINS-17267, add a Windows Batch build step:

mklink /d s c:\existingTargetFolder
mklink /j j c:\existingTargetFolder
md d

Build once. Then open Script Console and run the following script:

def s = new File(Jenkins.instance.getItemByFullName('JENKINS-17267').someWorkspace.child('s').getRemote())
def j = new File(Jenkins.instance.getItemByFullName('JENKINS-17267').someWorkspace.child('j').getRemote())
def d = new File(Jenkins.instance.getItemByFullName('JENKINS-17267').someWorkspace.child('d').getRemote())
[s, j, d].each {
  println java.nio.file.Files.isDirectory(it.toPath())
  println java.nio.file.Files.isDirectory(it.toPath(), java.nio.file.LinkOption.NOFOLLOW_LINKS)
  println java.nio.file.Files.isSymbolicLink(it.toPath())
  println ""
}
return

Output:

true
false
true

true
true
false

true
true
false

In other words, a pure Java program has no chance to distinguish between a junction and an actual folder.

I think there is nothing to be done beyond advising people to not use junctions.

jglick I think that this one has been resolved by JENKINS-29956.

FYI advising folks "to not use junctions" isn't viable - you might as well advise folks not to use Windows
Windows has hard-coded functionality preventing most people from creating Symbolic Links (you need to be a non-admin user who's been granted the right to create symbolic links, or you need to be running "as administrator" with no protection) and so the only remaining option is to use a "directory junction" (which anyone can create).
It's a pain in the ^%$£ but it's the only option for most users on Windows.