I think your problem is that your text uses Unicode encodings, but something somewhere between pbpaste, stdin, and ExtendScript is treating the string as ASCII.
The best workaround I can think of is to explicitly tell pbpaste to use a Unicode encoding, dump it to a file, and explicitly read the file back in with a Unicode encoding.
Sample code:
// create a temporary file
var tempFile = new File("~/TempUnicodeText-" + Date.now());
// pbpaste uses the LANG environment variable to determine its encoding
// we'll explicitly set it for a UTF-8 encoding, then dump the clipboard to a file
system.callSystem("export LANG=en_US.UTF-8 && pbpaste > " + tempFile.fsName);
// let's explictly decode our new file with UTF-8, read in the contents,
// and then delete the temporary file
tempFile.encoding = "UTF8";
tempFile.open();
var pasteText = tempFile.read();
tempFile.close();
tempFile.remove();
// now pasteText holds our Unicode-encoded string,
// and we can do whatever we want with it
alert(pasteText);