For Ubuntu I expect someone will create a PPA for Sun Java. I don't know if there's anything similar for Redhat/Fedora/Cent but wherever it's possible, I expect that will be the workaround of choice.
The way Gentoo handles this sort of thing (it does it with truecrypt) is keeping the ebuild and so forth around, but when it comes time to fetch the sources it will stop and tell you to go download the tar file from wherever it's usually at and stick it in the dist folder.
Someone will come along like sevenmachines and create a PPA with a "sun-java6-installer" to mirror the "flashplugin64-installer" that downloads the pack of binaries and installs them from Oracle's servers.
