If you find yourself confused about where a file really exists, cd to the directory you expect and use
rm -i and refrain from adding any path - delete the file in the current directory. Also, in unix, everything is a file - including a directory. You do have saving grace that trying to delete a file that looks like a directory will pause unless you are recursively deleting files.
Worst case, you could use
ls -lai to inspect the inode numbers to be sure a file is really symlinked and not hard linked.
If that doesn't help, make a temp directory and play with links:
ln foo bar # hard link
ln -s foo baz # sym link
At this point, you have the hard link file bar left and a sym link to the missing "foo" file. Since in your case, the link is in a different directory than the target, you shouldn't have too much problem deleting the item you wish.