Yes, just to be clear: items in the object window are
base objects. Items in the render window are
instances. However it's still possible for a script to refer to an instance of something, so you could still run into trouble.
If it's your own mod that has placed that instance, then you can delete it. If someone comes along and builds a patch on your mod, then they could run into trouble. Hopefully if that's the case, you'll know and you can inform them. In your mod, if you create a base object, you could delete that as well, with the same caveat about patches.
However, you should never delete anything in the Oblivion master, whether it be a base object or an instance because everybody will be using the same master file and you will cause trouble for somebody somewhere
For your info, btw, it is possible to create a mod without Oblivion.esm as the master, but those mods are rare and are rather specialized. You'll see a few more of those these days since Nehrim has been released.
Also as washington said, you can catch accidental deletions by using TES4Edit, but that should be something to catch accidents or to double-check your work. You should always clean your mods before release to the public anyway. The CS isn't perfect and dirty edits happen to everyone.