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There's nothing you can do about it. Calibre will try to use as much CPU power as it can get when doing tasks, as will any task. Couple that with CPU intensive conversions and you get the behaviour you're experiencing. You can change the thread priority for Calibre's worker threads in the settings, however, that will only influence how nice Calibre plays when other programs are trying to run at the same time.
Oh, and unless your system is overclocked and/or not cooled properly, 100% CPU usage isn't overtaxing.
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