ivwshane already covered what I wanted to say. I will add a bit more at a high level of generality.
Our constitution is written by human beings, with all their aspirations of good governance toward more perfect union. But the founders were humans after all, meaning that they wanted to have cake and eat it, too, just like we do. The Bill of Rights is not an internally coherent theory of rights, and the rights that we wish to have inevitably conflict with one another.
Take the recent controversy surrounding White Supremacists and their gun-brandishing rally. Does it have a negative implication on the 1st amendment right of counter protesters, bystanders, as well as the citizenry at large?
How about the ever-expanding reach of government surveillance. Would "exercise of the 2nd amendment," admittedly by some bad apples, have a negative implication on the 4th amendment's guarantee of privacy?
If private businesses and public institutions, understandably concerned about their bottom line in the face of murderous exercises of "the 2nd Amendment right," impose draconian security measures on patrons and citizens, how would they affect law-abiding citizens' sense of community as well as their own dignity?
Rights secured by the Bill of Rights are not absolute, not only because human reality sometimes demands their acquiescence, but because they often are not internally reconcilable. This is the context in which I stated the 2nd Amendment right at some point must give ways to the rest of the Bill of Rights.
I do grok what you're saying, and there are some inconsistencies that the SC has had to clarify/define as time has progressed. I personally think there's some holes in some of your specific circumstances though.
Gun brandishing rallies: Freedom of expression and right to be arms are fine here. It doesn't have a negative implication on anyone else to include counter protesters, bystanders, or citizenry, unless one of the nutjobs opens fire, at which point he's committing a crime (as any other). You might say that the threat of violence tempers the counter protesters/dissenting voices, but only if fear is guiding them. Futhermore, this is a private organization (white supremacists) not the US govt, which the rights are codified to protect against. There may be some gray area in there somewhere but I personally feel that an individual with a gun isn't a threat unless they're planning on using it, and if we're assuming that these particular individuals have no intent to use them, then there's nothing impinged on by them. If they use them, they're committing a crime anyhow, so the 'they're suppressing our 1A rights' kinda goes out the window.
Govt Surveillance: It only has a negative implication if the govt does something about it. Exercising 2A rights themselves doesn't require the government to increase surveillance, they're independent events. Devaluing/eroding the right to one's person is protected by the Constitution, and the Govt is *supposed* to not be allowed to do that, regardless of secondary or tertiary events taking place. Having said that, this one's been probably the hardest hit in the last 50 years.
Private/public businesses: It's been shown multiple times that Constitutional rights are defined as what the govt can/cannot do, not private citizens. Now this gets fuzzy in things that are semi-mandatory, such as a local utility refusing to deal with African Americans, for instance. The courts have been known to 'overextend' a bit to ensure the equality and liberty of individuals in the face of other individuals who would impinge on that right, but it's not super common. It's also happened in more pedestrian cases, as we're going to see in this SC cycle, they're addressing that whole 'no cakes for gays' event a few years back.
You may be entirely right that the 2A rights get reigned in, in theory, to protect other rights. I personally feel that would be a mistake, but part of the wonderful thing about the US is, we get to remake our rules as the Union sees fit, rather than have them written in stone by a King, and enforced under pain of death.