That re-enabling itself is exactly the frustrating part — disabling it once clearly is not enough if an update puts it back in Startup.
On your question about the standalone install: no, updating a standalone install should not bring the Assistant back. The Assistant is only bundled with the standard installer, which is why burnout426 suggested a standalone install in the first place. Its own updates update Opera itself; they do not re-run the standard installer.
So if you do try that route, install it standalone in its own folder and do not run the installer as administrator, then check Task Manager > Startup apps and Settings > Apps > Startup after the first update, just to confirm it has stayed off. The trade-off burnout426 mentioned still applies: a standalone install is not registered as the default browser, so you would need the Portable Registrator tool susanm mentioned if you want it as your default.
If you stay with the standard install instead, I would check Startup again after every Opera update, since that is when it seems to come back for you.
