</tinfoil hat>
If all the executables in the archive were, say, loop-free trivial programs, then of course you could instantly confirm an absence of malware.
If there are some loops and complications in there, you would do some more logical work, and then depending on the power of your logical system, either conclude safety or unsafety, or time out.
Rice's theorem does not mean that static analysis is impossible, even of machine code!
The fundamental limitations of computer science, as expressed by Rice's theorem, says that the CIA cannot make a program that given any archive says in finite time whether there is malware there.
It doesn't say that for some specific archive the CIA cannot guarantee the absence of malware.
There are infinitely many EXE files that you can prove malware-free, and this set expands with the progress of static analysis.
But of course, if one EXE file says "if (unsolved_math_problem()) { malware(); } else { harmless(); }" then the CIA would have to spend a lot of effort proving its status.
The CIA cannot guarantee that files they have spent 6 years poring through are free off malware? Wonder why anyone will download these documents after this.