Is eating bread immoral?

I think there are two important questions here:

1. Is eating bread bad for your health?
2. Is it immoral to do things which are known to be bad for your health?

As for question 1, there is a lot of evidence out there that certain people (perhaps even many people) react badly to gluten, and should avoid it completely. There is also evidence to suggest that many more people would probably be better off if they avoided it as well. I'm no expert in nutrition (and such a question is certainly beyond the scope of Objectivism!), but I've not seen enough evidence to convince me to stop eating bread. Perhaps more knowledgeable people will be able to fill in more details about gluten.

As for question 2, It depends upon what values are most important to you: within reason. If the risk to one's health is not 100% certain, or if the risk has mild consequences, then it is certainly rational (i.e., moral) to assume that risk. Over time, drinking alcohol has alternately been seen as very dangerous, to neutral, to beneficial (for red wine): definitely not 100% certain. Being mildly overweight (5-10lbs) isn't great, but the consequences to your health aren't huge. On the other hand, being an absolute tee-totaler or going on a constant and severe diet would seriously impact some people's enjoyment of life. For those people, it would not be rational to make that choice. For someone who wouldn't miss those things, it would make sense for them to adopt that sort of lifestyle to enjoy those benefits. The principle is that a person should maximize their long-term happiness, and that can only be done by weighting the pros and cons of both options over the long term.

Of course, there are things which go beyond merely being "risky", but are flat-out dangerous to the point of being suicidal: russian roulette, rock climbing with no ropes or training, or playing chicken with freight trains. Such actions aren't merely a question of one's optional values. The extreme likelihood of extremely dire consequences makes it irrational (i.e., immoral) to pursue them.

When Objectivism condemns something morally, one usually finds adjectives that are considerably more colorful and descriptive than merely "immoral" -- such as "evil," "despicable," "unconscionable," "disgusting," "monstrous," "contemptible," "anti-life," and so on. For lesser moral offenses, simply identifying them as "self-destructive" is usually adequate. One would be hard-pressed to classify bread eating as self-destructive, however, given the excellent nutritional benefits it can offer, especially whole wheat bread, for those who do not have any unusual adverse sensitivity to the gluten or other ingredients in it, as most people don't. It would be rather fantastic and ridiculous to condemn people morally for eating bread, unless one is severely allergic to it and eats it anyway, knowing one's intolerance for it (or eats too much of it willfully). The question itself acknowledges that the alleged harmfulness of bread is only "purported," not proven (and not universal for all humans). "Ridiculous" can be regarded as a moral evaluation, also, if done on purpose and not meant as humor.

As for choosing other food types over bread for even better nutrition, that would be an issue of how best to sustain one's life. Refer to a separate, very recent discussion of the "Paleo Diet" on this website.

I answered this question in a recent edition of my Rationally Selfish Webcast.  An audio recording of my response is available as a podcast here: NoodleCast #56: Live Rationally Selfish Webcast. The discussion of this question runs from 50:24 to 1:00:00. 

My basic view is that while health is not an optional value, a person's diet cannot be a moral issue absent some evasion.