The only time intent can be proven is once the act, presumably a harmful one for the sake of my argument, is committed; but then there is no justice to be had anyway because entropy is lost, thus only revenge and/or correction is left. But back to my counter argument, the possibility for harm is a flimsy definition of a crime and runs against the principle of reasonable doubt; cars are pretty harmful, I myself drive past children I could deliberately run over and probably kill on my way to class (college) everyday (I'm not going to do this; but then again you only have my word...) and thousands of people die in them and by them every year; my point is that guns/cars have other legitimate uses and the same could be said of things everyone already has possession of.
Also, your previous arguments that owned hardware which is at least somewhat controlled by the owner (otherwise, who controls it "owns" it), thereby implants guilt onto the owner is also, well, incorrect. While true that the individual or organisation are generally responsible for the operation or neglect of their hardware, in the case of hardware whose explicit purpose is to service requests to uncontrollable and external parties and is thus to a certain extent designed to be deliberately neglected, can't be held responsible for crimes for which they had no participation in: I am not responsible for the crimes of someone who stole my car beforehand (the involvement of theft makes this example a bit shaky, I'll admit, but my point is to convey the separation of responsibility between owner and controller, in that as the owner I didn't encourage the controller, the thief etc, to steal my car). That said, imparting a bit of responsibility onto owners is still a Good Thing (see workers comp.), because it incentivizes safer workplaces/hardware: the difference is that in the aforementioned case, barring proof of intent or neglect, it's not a proper crime, it's just monetary damages (ie civil).
Just to be clear, we agree that something like smallpox should stay locked up. But then every sane and rational person should agree with that: they would have to live (note sane and rational) in the same world with smallpox on the loose. But then if it did get out, due to it's infectious and self-replicating nature, the result would be disastrous. In any case, such eventuality would either be the work of an insane or troubled person (whose actions aren't rational anyway, thus can't be called 'our' fault, presuming attempts to prevent the release were made) or an accident. In all cases, punishment isn't the answer (except in the accidental case, the answer is instead institutionalization). Nonetheless, the solution to prevention of eventuality in this case is access limiting. Thus it is an acceptable solution. (I consider this to be a satisfactory rationale). But even quarantined diseases are still studied!
One last thing: brandishing a weapon is a crime by way of implied speech: it is threat. Thus brandishing a weapon is an action, and is thus not just possession. Which means it doesn't count.
TL/DR: The condition (possession -> guilt) is false. Punishment for such possession is unwarranted. Control is implicitly limited by sane and rational owners in the case of dangerous Things (perhaps with the help of others).