I doubt you'll find any virus which is completely benign (even fixing a vulnerability after exploiting it is still malicious behavior, even if it is intended to be beneficial), but there are plenty of examples of exploits which are. The most well-known would have to be jailbreak exploits, where a vulnerability in a proprietary and closed system is attacked intentionally by the owner of the device to "root" it and gain better control.
In the past, people released malware (viruses, worms, etc.) for fun. Some people would be particularly malicious, with their software corrupting files or rendering a system useless, whereas others would be relatively harmless, doing nothing more than spreading (sometimes too fast, which does cause harm). Back in those days, people would also occasionally release viruses which attacked other viruses. In fact, the Creeper virus you mentioned was attacked by another virus called the Reaper, which did nothing but attempt to remove Creeper infections. Of course, it was still a virus, so it can't be called entirely benign.
Another example of a "friendly worm" would be Welchia, which spread automatically through networks, patching the DCOM RPC vulnerability used by the infamous Blaster worm. Nowadays however, most malware is made for profit, and the historical "malicious mischievousness" is far less common. If you ever see a worm or virus which attempts to destroy existing infections today, the purpose is usually to destroy the competition so it can run its own payload. Some malware calls this feature "mini-AV".