That's absolutely true. Neither a corporation nor an individual can engage in libel, some types of obscenity, true threats, etc. Furthermore, there are indeed cases where corporate entities are treated differently than individuals, and no one seriously argues that it's inappropriate to do so (there's no corporate right to bear arms, for instance, and corporations don't cast votes in elections). On the other hand, there are obviously very important situations where a corporation must be treated as a legal "person" (to sue and be sued, to own property, etc.)
The crux of the argument that won in Citizen's United is that, among all types of speech, it's political speech that must be jealously protected. Even though there are serious arguments against allowing corporations to participate in campaign-related speech, it was found that there was not enough of a compelling government interest to overcome the strict constitutional scrutiny that is required when the government seeks to limit political participation. As corporations are just groups of people who form an entity to pool resources and share in ownership, those groups of people do not lose their rights because they pick one social and legal structure over another (for instance, a school, non-profit, or a church). The important example was of a corporate entity producing a video that was critical of Hillary Clinton within some amount of time before an election.
The "you cannot yell 'fire' in a crowded theater" argument makes it seem as if others are denying that the government can regulate any speech, but that is not true, people understand the current state of the law.
I think I can rephrase your argument as: "I cannot shout 'fire' in a crowded theater, so obviously some speech can be prohibited. Therefore, since we're only talking about where to draw the line, it can be drawn over here where I'm advocating it be drawn." This ignores distinctions between situations that have been acknowledged for a long time. You cannot shout "fire" (falsely) in a crowded theater because it would be illegal to say something false when you know it is likely to cause immediate harm. It is also illegal to do other things that are kinda-sort-of free speech related if you look at them the right way -- you can't lie for financial gain, you can't lie to obstruct an investigation, you can't lie under oath, you can't file a false police report, etc. etc. Because these are all true, it doesn't mean that in a different situation speech can necessarily be regulated because we've already crossed the line out of absolutism and into situationally-dependent regulation.
Reading your post helped me think of a more concise way to say this. So thank you. And again.. I am not really sure and I see both sides.