Which did you see as the conclusive evidence that code was copy-pasted? Section 4 of the article made the point that the Rybka source was missing and the accusers' evidence was decompiled code which they had arranged to look as similar as possible.
Yes, section 4 says that, but I do not find that section convincing. IMO, some of its arguments are flawed. For example:
"integers are quicker than floating-point numbers"
Maybe in this case, but not in general, on all current hardware. Chances are that chess programs use little floating point code. If so, using a few floats here and there can even be faster because it allows the CPU to issue more instructions in parallel.
"According to Rajlich, he wrote a utility program (separate from Rybka and not available to users) in the C# language to generate his PSTs. As Fruit is written in C (not C#) this means there is a 100% certainty that Rajlich did not copy the Fruit PST generation code."
For low-level chess code (a bit of bit-twiddling, array lookups, arithmetic, but no library calls), I would think that porting C to C# can be an almost 100% copy-paste job.
Remarks like these make it hard for me to accept the conclusions as undeniably true. The "but everybody is doing it" argument, on the other hand, I found more convincing.