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:

touch foo
ln foo bar       # hard link
ln -s foo baz    # sym link
ls -lai
rm foo
ls -lai

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.

Here's the script to find and remove trailing space from files and dirs:

#!/bin/bash                                                                                                                                                                                                        

IFS=$'\n'
for file in $(find -d . -name "* ")
do
  target_name=$(echo "$file" | sed 's/[ \t]*$//')
  if [ "$file" != "$target_name" ]; then
      if [ -e "$target_name" ]; then
          echo "WARNING: $target_name already exists, file not renamed"
      else
          echo "Move $file to $target_name"
          mv "$file" "$target_name"
      fi
  fi
done