For the pdflatex version, you seem to be having
the same problem discussed here -- apparently in order to use classicthesis with utf8 characters in section titles (--notice there's no problem if you use unaccented latin letters only--), you need to use the pdfspacing option for the package. You have that option commented out, but it seemed to work if you uncomment that option.
I noticed, however, that even with nochapters it seems to want to print a 0 for the chapter number before the section number anyway. I guess you could fix that by putting:
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right before \begin{document}. This should suppress that 0.
For the XeLaTeX version, it's a bit trickier, since I cannot recreate the problem. When I compile your file, I don't get that error. (And it fully stops compilation: so it's not that you aren't getting the Cyrillic characters; no file is being created at all.) I guess there are some differences in our set ups. I'm not sure what it is. (You're using TeXlive 2009 for Debian/Ubuntu; I'm using TeXlive 2010 installed from TUG, though I don't think that alone explains it.)
Looking at your log, however, the problem
seems to have something to do the pplj font, which is one of the Palatino fonts classicthesis wants to load with the mathpazo package. Especially since you're overriding that font anyway, it hardly seems like it should matter. But it does. Since you're modifying the .sty file anyway (and creating a local version), you might try modifying it further by removing the line (line 187):
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from classicthesis.sty (--you want want to remove the line after it too depending on the font you end up picking and whether it seems to require greater line spacing).
Probably you'd need the other changes above for handling the section numbers and titles here too.
Good luck!
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