With TortoiseSVN, if you simply delete a file then it becomes "Missing". If you delete a file in Eclipse, it tells Subclipse you deleted the file so it runs svn delete. The equivalent of taking the Delete action in TortoiseSVN. When you do an update, missing files are restored in your working copy, but deleted files are not -- because you said to delete it.
You are getting something else though. In your case, there was a newer version of the file in the repository. Because it is marked deleted locally, that is a tree conflict. If you did the Delete action in TortoiseSVN you would see the same.
The tree conflict is so that you are aware that the file you deleted has been modified by someone. So maybe you want to reconsider the delete etc. The Team > Show Tree Conflicts option will show all tree conflicts and provide option to resolve it.