You're talking about two types of security:
- Confidentiality of the SSL connection which depends on the private key being available and
- System integrity, which gets compromised before a private key becomes vulnerable.
The SSL connection that is established between clients and web servers depend on the private key being available so that it can complete the session key exchange.
If an attacker gains access to your system and gains elevated privileges, sure the private key on the filesystem is low hanging fruit, but a super user can also MMAP_PHYS in all system memory and scan it for the keys with just a little bit more trouble.
So, no, deleting the private keys would not prevent private key recovery (from memory), except if there's a power outage, reboot or something like that. Basically system integrity MUST be assured to keep your system resources (keys) safe from intruders.
Is this design just a bad example of security through obscurity ?
No, not security through obscurity. SSL is based on sound cryptographic concepts. Security in depth mandates that the private keys (read: system integrity) are protected by other layers of security such as mandatory access controls.