Of course this fungibility is not an issue, until either a government or individuals begin to engage in a practice of changing value of coins based on demarcation, which is currently not an issue, but instead a speculation of an issue that could come up perhaps maybe blah blah blah. And, also assuming that there is no way to remove history, then there is a way that coins could begin to look distinguishable from their history... but so far remains a BIG SO FUCKING WHAT?
For me, the dream of fungibility died when Ross Ulbricht went to prison.
But wait... Isn't fungibility a matter of degree rather than an absolute? It seems to be like a moving target phenomenon in which government and anti-bitcoiners are going to want to place these kinds of restrictions on bitcoin in order to lessen its value and utility; however, developers are going to continue to create vehicles, and users are going to find ways to take advantage of tools that are provided... so in the end, who the fuck cares, if some coins that you have started with silk road, once you get a few levels removed from such. And, maybe white washing coins will become a more prevalent practice, even through lightning network, perhaps? Perhaps?
Scaling is a similar subject matter. There is likely going to be a continued issue about scaling that has to continue to be adjusted for the level of use and the degree to which there are "scaling issues."
In the end, bitcoin is not likely to be broken by either fungibility issues or scaling issues because development and tricks continue to evolve while maintaining some foundational bitcoin principles (in terms of design and operation).