In general, Opera lets the user configure whether it should respect autocomplete=off. On principle, users should be able to configure the password storage feature, and web sites should not be able to affect the configuration at a whim.
However, I can certainly see that for specific scenarios, like "send one-time passwords by SMS to the device Opera remembered the regular password on", this sucks. If you have stored password for a high-value site + use SMS one-time passwords as an "out of band" authentication, a lost phone becomes a major risk. The root of this problem is the assumption that an SMS constitutes "three-factor" authentication - if the stored login and the SMS is on the same device it's no longer "three-factor"..
It is tricky to try to leave users in control, while yielding to the web site when it's a really good idea to do so. Sadly, I think this is an unsolved question for now.
If you have a good use case for disabling password storage and are working on an important site, perhaps Opera Mini server admins could be persuaded to disable password manager on a site-specific basis? I don't know, but if you report it as a bug to Opera it would at least give the internal discussions some more momentum. Feel free to contact me with a reference to the bug report because I'm in a position where I could keep an eye on it ;-)