If you're paranoid, you may want to run an ONT that you control, just in case. I doubt it's something that matters to a lot of people, but even if it only matters to some, it shouldn't be made impossible for those that want to.

RE: misbehaving hardware: the same is very much true for cable internet and there are plenty of countries where people hook up their own modem without any trouble. If someone wanted to mess with the fiber network they could just disconnect the ONT and shine a laser pointer down there. All off-the-shelf devices are built to just work and follow the necessary standards, because there's nothing to be gained by messing with the PON network like that.