APPROVED ANSWER
replied on February 3, 2015
Hi Bryce. We're reviewed the bug filed for this issue. One thing that needs to be clarified is that overwriting an electronic document is different than deleting an electronic document. In the situation you described where the user imports an electronic document into the repository that already has an electronic document with the same name and chooses to overwrite, this is allowed if the user has the "Modify contents" right on that existing document. This process is the same as if the user had opened the original existing document in the repository, and then copied the data from the new document and pasted it back into the original document, overwriting the old data, and then saving it. Deleting doesn't come into play here. In both situations, the electronic document component isn't getting deleted. New data is just overwriting existing data in the document.
If you're concerned about protecting against accidental overwrites, you can deny users the ability to modify contents, but then that most likely limits their productivity.
Please let me know if there is another concern that you feel isn't being properly addressed. If you can provide details and a use case, that would be helpful.