Glad to see I'm not the only one but it stinks you're going through the same pain.
I followed these instructions to remove the 1.6 JDK from my MBA and while it doesn't remove the symlinks, it at least got Apple's JDK off my system:
Now, when I go to terminal, I get prompted to install Apple's JRE.
My solution was similar to your's except that I worked with the developer of Charles and he provided me a version that has the latest Oracle JRE prepackaged into the app. It doesn't install anything at the system level and is completely self-contained. So this effectively allows me to remove Java completely from OSX and not worry about any Java exploits at all.
I've asked him if he could provide any understanding of why using Charles prompted the dialog and if I get that, I'll post here as well as my other thread which is related to this specific issue:
If you do find a way to identify all of the loose symlinks and remove them, would you mind posting that as well?
No, it doesn't. I stopped thinking about it long ago. It's one of those weird things in this world that simply "should be fixed". It's bizarre if it carries on even in Java 8 time (I do wish not).
It's two commercial corporation doing stuff. We probably don't have similar examples in the open source world, do we?
So, I have Eclipse working w/o installing Apple SE 6. Simply install the newest version of Eclipse 64 bit and JDK 7 and they "just work" without any other problems -- apparently the older version of Eclipse that got copied over with my profile from my previous machine couldn't do this, but the newest one can.
The only problem I have left is that Max for Live requires Java and it doesn't seem to be clever enough to avoid the problem. I'll take that up on the Ableton forums and see if anyone has a solution there.
I REALLY don't want two JRE's on this machine if I can help it.