Glenn,
There are, broadly speaking, two sorts of reasons to bring to bear on this comparison. One sort is consequentialist, which is to say reasons having to do with how well off people will be (or not) as result of either policy. The second are, unsurprisingly, non-consequentialist, which can appeal to a range of factors but here will mainly appeal to the rights of individuals.
Now, yes, rights of individuals legally speaking are often justified morally on consequentialist grounds, but I'm going to ignore that for the time being. I'm going to assume that a right is a (defeasible) reason to place against the claim that things would be better all things considered if some action were done. That will just make things simpler.
When it comes to drugs, the prohibitions are paternalistic in nature. Paternalism here will just mean restrictions on people for their own good. Paternalism might be challenged on consequentialist grounds. It might be argued that people are all things considered better off if they can decide rather than the state whether they will take drugs because they can better judge what's in their own interests, or it might be argued that the prohibition is inefficient even if the state knows best what is in drug users interests. This second reason is powerful, as evidenced by all the discussion above regarding incarcaration costs, violent crime associated with the illegal markets, etc.
There are non-consequentialist anti-paternalistic arguments. Basically, they maintain that even if things would improve all things considered the state has no right to coerce people not to take drugs. People have a right to decide what they want to do with their bodies even if it is suboptimal. This kind of point is often made when it comes to people's decisions to have relationships that seem obviously bad, do things like mountain climb or sky dive, eat unhealthy foods, or whatever, where it's clear that there are choices with a greater expected value for the person, but which the person rejects. In any event, this is the type of non-consequentialist reason brought to bear. People have a right to engage in the self-affecting behavior of their choice even when it is clearly suboptimal, or even outright bad.
Guns are not quite the same thing. The consequentialist arguments are similiar in many ways, but different in important respects too. I won't rehash them here. But non-consequentialist arguments, if there are in fact any such, are very different. For one thing, restrictions on guns are not primarily argued for on paternalistic grounds. They're argued for on the grounds that a legitimate market in guns aids criminals in their acquisition of the means of injury and murder, in one way or another. So, this puts them under the heading of restrictions enacted to prevent harm to others, not paternalist restrictions. Granted, the harm in question is indirect. Proponents of restriction would say that the harm a gun owner causes by buying a gun is the small contribution to the market which the criminal is a parasite on, either through theft of legal guns, or fake purchases, or legal purchases for nefarious ends, or whatever. In this way it's something like the harm of dumping a small amount of carcinogen into the water, in that by itself it's no big deal but combined with the actions of others it's very harmful. But still, it's an activity which contributes to harm to others and so on that basis should be restricted, they would say.
So, the non-consequentialist anti-paternalistic arguments against drug prohibition are not direcly applicable here. Whatever non-consequentialist argument one would give must be of another sort. One possibility, of course, is that _even if_ it made things worse the state has no right to interfere with a person's right of self-defense. That is, much as some civil libertarians argue that we have rights against search and seizure which should be respected even if their disregard would reduce crime some amount in the long run, so too do some gun rights advocates argue that we have rights of self-defense which the state should not infringe through gun restrictions even if that would reduce violence by some measurable amount.
There are questions associated with this sort of argument. Is the restriction on the use of particular weapon an infringement on the right of _self defense_ if defense is still permitted under the law? Is that right the sort that should be considered to have significant non-consequentialist weight? Etc.
I don't mean to get into these issues here. I think they're tricky but interesting. I just point them out to show that in considering the difference between the drug prohibitions and gun laws different principles will be at stake from a non-consequentialist's perspective.
That's what I have to add on this topic.