You're looking for a digital answer in an analog world.
Any system of justice is going to be flawed. Period. That's a given, going in. It's even more certain than "The new MMO is going to have launch day bugs."
So, given that, we (all human societies) work to find the least flawed approach, defined as "the guilty get what's coming to them, and the innocent go free and suffer as little inconvenience as possible". (We're really screwing up that last part, with 2+ year waits for trials in many case, but that's another thread.)
We have the system we have because centuries of history, precedent, and experimentation have shown it works as well as anything else, and the risks of radically altering it outweigh the perceived gains. There's plenty of reasons -- people have historically been tortured into confessing, but not into witnessing. Intimidating witnesses is a lot easier if the witnesses have no legal pressure to *be* witnesses. (IOW, Big Vinnie is arrested. If his boys want to silence the mooks what seen him do it, they have to bribe them/threaten them. Obviously, this does happen, but the cost (the value of the bribe, the severity of the threat) increases when the witness knows he will be compelled to testify and can go to jail if he doesn't. Big Vinnie's boys have to overcome that resistance. Remove that, and it's a lot easier. They probably don't need to EITHER bribe (which saves them money) or directly threaten (which puts them at some risk if one of the mooks has a wire). The mere knowledge that they might not take kindly to someone ratting out Big Vinnie is sufficient for the witnesses to refuse to testify, if said witnesses cannot be pressured or compelled.)
Further, if witnesses must give testimony, it is easier to spot conflicting details that can show a witness to be unreliable (or simply human, as the fact is, most people are unreliable and conflicting eyewitness testimony is rarely as dramatic a proof of a cover-up or a lie as it is on TV). If every witness just says, "Nope, don't feel like answering.", then you have nothing.
Now, an argument can be made that if the justice system is weighted towards innocence, neither of these is overly bad; it will result in fewer convictions. However, this could tip the balance too hard against conviction, and when there is a perception that you can do anything and get away with it, there will be a mass movement to "tighten things up", and swing too hard in the other direction. I'm honestly not sure of the real effect on crime, at least not serious crime, because such crimes are rarely conducted on a rational basis. A study of NYC street criminals showed that, basically, they earn minimum wage in terms of hours worked (waiting for victims, etc.) vs. average "take" -- and faced extremely high occupational risks. Most murders are acts of passion that are unlikely to be repeated, and other than the very few professional hitmen out there, few consider a cost/beneft ratio. Murders committed in the course of other crimes (shooting a store clerk in a robbery) are insanely irrational -- you get a few hundred dollars, maybe, from the cash register, and risk life imprisonment or execution in exchange. The real function of the justice system is not to deter crime, but to remove from society, for a long period of time, those who are so irrational that they WILL risk years, decades, or their life in prison for a very small gain, or are so uncontrolled they will kill or beat someone in a fit of passion. If you accept this premise, then, compelling witnesses helps fulfill the goal of being sure this person is the one who should be removed from society.
It also serves as a protection from an overzealous state. If the only evidence is provided by the state, and the defense cannot compel witnesses, the jury will have no choice but to convict. With zero penalties for failing to speak, witnesses may simply not bother. Why show up at all? (And, in turn, this leads to a possibility of basically bribing witnesses to show up -- not to lie, which is a higher moral bar, but simply to show up in court at all, if they're free to say no.)
None of these arguments are without flaw. I could pick them apart for you myself, but I'm running out of time. :) The real answer is, basically, "Because this system works pretty well, as it is, and the risks of radical change outweigh any proposed benefits." You want to change the system? Don't ask "Why are we doing it this way?", but say, "Here's a BETTER way, and here's WHY it's better." Then, people will have to defend the system as-is against a concrete, defined, alternative, and confront the justifications of the existing system in terms of the problems your new system is supposed to solve.
At a certain level, all social structures are arbitrary and irrational and fueled by inertia. Our society has internalized the flaws in the current system and learned to live with them. Any new system brings with it unknown flaws and a long period of adjustment. When you can offer a high probability your new system will have fewer flaws, and that they can be adapted to relatively quickly, society might embrace it. Until then, "We're doing it this way because it works well enough" is really the answer. You haven't shown a *benefit* for changing. Your entire argument seems to be "But this is just random and arbitrary!" Yes, it is. After thousands of years of civilization, the "design space" for big, sweeping, ideas in justice systems seems to have been explored. What's left is a collection of core ideas shared by most of the world, and fuzzy details at the edges which are basically random picks from multiple choices whose benefits and costs roughly balance.
(The idea of special protection for journalists has justifications, as well -- because systems inevitably become corrupt, because people become corrupt, and one of the checks and balances on this is protecting those who expose corruption... but often, those involved in providing such protection are, themselves, corrupted. Thus, being able to not name witnesses or sources serves as a vital tool for preventing corruption before it becomes too extreme, a pressure valve, if you will. The counterbalance is that anonymous sources come with a lack of credibility, that people will be disinclined to take nothing more than "I know this guy who told me this..." at face value. Anonymous sources who provide verifiable data, OTOH, are vital to the functioning of democracy as we understand it, and protecting all those in the chain of evidence from legal and extra-legal payback provides very high benefit at very low cost.)