What is timing out, Spamsieve or my AppleScript?

As I said, you can record a sample to see why SpamSieve is timing out or suppress the error to avoid the dialog. (It’s being shown by whatever is running your script, not SpamSieve.)

For example, you could write:

try
    set _score to score message _source without auto training
    -- Other stuff that depends on having the score
on error _error
    my debugLog("Error: " & _error)
end try