I don't recall the "install new updates" feature ever offering to perform a major release, certainly not without explaining that it's doing so like just happened with Juno. I unintentionally updated and it appears to have done an in-place update. This whole process is new behavior, right?
Is there any way to safely downgrade back to Indigo?
Get a copy of Indigo and unzip it to a new directory.
Add your other Eclipse plug-ins from their web sites.
Zip up your newly created version of Indigo so you can restore it if you accidentally upgrade again.