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I don't disagree that this happens or will happen but IMO the issue as you present it is a construction of fiat parasites especially interested in undermining the privacy and fungibility of Bitcoin.
As we slowly move away from this paradigm I believe it will eventually become a non-issue. Moreover I understand there is significant progress being made toward implementation of privacy related features in things such as sidechains which contribute to solve the related issues.
I agree that this is exacerbated by "fiat parasites", but I disagree it comes only from this.
Even in a fully Bitcoin-based economy, I don't see why it would disappear. You could still refuse to deal with coins out of belief or social pressure. Think of the US dentist who went to kill this lion and was everywhere in the news: imagine if he had paid for the "right to kill" with bitcoins, that the entire world would know at a given instant would be on an address X. Don't you think some people out there would refuse them for a payment?
I believe it will always happen, if you can attach history to coins (in practice outputs).
You could also refuse to deal with coins out of legal fear. If you own anything (money or objets) that you know is coming from a theft, you're legally liable as well (fence in English?). If you don't know but didn't take sufficient precautions, and the circonstances should have raised suspicions from you, you're liable as well; at least where I live. Why would the legal system be any different with coins? In fact it's worse: it is much easier to do your due diligence with bitcoins than with real world items, so you can be also accused more easily.
EDIT: I forgot about sidechains. A sidechain implementing "confidential transactions" would help with privacy (despite not providing untraceability - that is not hiding the origin of the funds). But they don't solve fungibility: they could be seen like a mixer, and with limited liquidity. Coins seen entering in to be made more private, then seen going out. It is easy to be "hey why did you sent coins to this sidechain?", or "I don't want coins that visibly were mixed on the sidechain!".