As I said, people use copyright law to take other people to court, and then get money from them. Your "fuck copyright" statement is bold, and one I'd generally agree with, unfortunately it has zero relevance to the legal risks a business would take, using this code in a commercial product, in such a country.
As the author said, the files violating copyright are easy to replace. Let Skype ask for it, it will be 2 more days of work.
The reason why people want to see a clean room implementation is because they are afraid of patent and anticipate US-like silliness like Oracle claiming copyright on an API. Now that this is a very US-specific issue. If you don't plan to market to US, you can just ignore the issue.
I used to work for a French AR company. We were successful and at one point we planned to open offices in the US, but even without having done that, we already had received two frivolous claims by people based in the US (one who claimed he patented the idea of replaying the video at a varying speed). This delayed a bit our opening to the US and the first US employee was... a lawyer.
Do you realize that patents and copyright hell is the reason why, for more than a decade, VLC, a project made by French students, was better at playing videos than Microsoft's player, even when this was seen as crucial? Because France did not have to care for patent litigation.
Patents are another issue. Doesn't specifically affect this project.
And clean-room implementations have no effect on patent violations or claims. None at all. It is entirely a copyright issue. And the issue here is that the same person who disassembled one codebase then wrote a new, equivalent codebase. Thus the new work is a derived work, or at least a lawyer can argue that easily, and thus distributing it for profit is a serious crime. Not even a civil offense, in any EU country. Criminal.
I live in a EU country where interoperability is a law yet is almost never respected, so I say, fuck copyright in that case.
However, this is not the first successful reverse engineering of skype. Each time they broke compatibility with their next version.