You can remove /dev_hdd0/game/LAUN12345 by using the FTP.
Some people speculate that the PS3 logs all games played (similar to the Wii) and then uploads that to Sony later on. If that exists, the location of it is not yet known as far as I'm aware, although it would no doubt be uncovered with time.
If you're really concerned, you could backup your game saves and then reformat and do a factory reset to defaults. That doesn't guarantee that something wasn't stored in the Flash though.
All that said, even if you ninja'd Backup Manager, there still is plenty for Sony to detect and log. For example, the 360 is hacked via the drive's firmware and yet MS can detect subtle changes such as disc loading speed. If you use the jailbreak, I think you should expect that it can be detected no matter what you try.
The only 100% sure option is to stay offline. Pick up a second PS3 and use one for jailbreaking and the other for legitimate (ie. Sony sanctioned) use.