Is there a way to remove/hide this option from the drop menu when you right click a file from the "Project Media"?
The issue is that it's located right at the bottom of "Remove from Project", and there's a chance that you might one day click on the wrong one without knowing it, and once it gets deleted, it's permanently gone. You can't even find it in the recycle bin.
I doubt that the options appearing in the drop down menu are removeable, but the circumstance you raise (accidental deletion) highlights the importance of always having at least one copy of all your original video/sound/images/renders on at least one other media (e.g. external hard drive). Having a backup makes an accidental deletion via your NLE an inconvenience rather than a disaster.
At least you get one of these warnings* before the file is permanently deleted. (The one on the right if it's on the timeline already. If it's not you get the one on the left but need to use undo to get it back as it's removed from Project if you choose No or Cancel)
*) "Warning: Important information that you need to know before performing a task." (from online Help)