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A timeout wouldn't change your situation either. The conversion would stop, but it wouldn't be finished, so you'd have no converted book.
Your fan switching to higher RPMs isn't necessarily bad, that should happen if you're running CPU intensive tasks, which a conversion definitely is. If you feel your system is getting too hot, try monitoring the temperature, but that would be a hardware problem, not a Calibre problem. Computers do enjoy getting the lint removed once in a while, by the way...
Edited to add: As far as I know, conversions are singlethreaded, so if you start only one conversion, it'll take (mostly) the same time as when you'd start as many as you have cores available.
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