If you can't set the number of cores used by the application: create a virtual machine, assign it only a single core, and have a blast. Performance will only be about a quarter of what you would get with all four cores, but the load on your machine will be lower, resulting in lower temperatures and quieter fans.
Although I wouldn't worry too much about the high temperatures. Yes, 100˚C sounds high, but remember this is only a very local measurement at the actual cores of the CPU. In a tightly-packed Macbook Pro the CPU cores quickly reach ~98˚C, but the CPU proximity remains at about 55˚C (about 20˚C increase compared to idle; this number is roughly equivalent to heat sink / CPU casing temperatures reported by most desktops). What about the SSD and batteries in the Macbook? They increase with only 1˚C to 28˚C. It's like lighting a cigarette lighter in a room. The flame is hot, but the rest of the room in not melting away.
Regarding all these worries about high temperatures. I'm not an electrical engineer, but my guess for all these worries is that back in the old days with electrolyte capacitors high temperatures (say >65˚C) would drastically reduce the lifespan of your system as it could potentially cause the capacitors to rupture due to increased pressure caused by the liquids. However, with miniaturisation of electronic components came the solid-state capacitors that no longer use liquids that can come to a boil at high temperatures. Consequently, these capacitor have been rated at a safe operating temperature of up to 125˚C. Safe operating temperatures defined by Intel are guaranteed by throttling the CPU.
P.S. I'm not saying temperature does not have an effect of life span of electronics, but I don't think the impact is as significant as it used to be. I love to let machines crunch numbers and process data, and I've had many machines operate at high temperatures. The best memory is of a small form-factor Shuttle casing with a Pentium D 950 (about 135W if I recall correctly) that would run at >105˚C (back in those days the software tool would only show graphs going as high as 100˚C). It was packed in a small wooden cupboard, and when you got close you could actually feel a difference in temperature (although we are already sensitive to temperature changes of 1˚C). It ran for four years straight until a power surge killed the system (killed the PSU and fried the motherboard somewhere near the memory sockets). I transferred the CPU to another computer and it lasted for three more years before finally giving out after moving the computer to a new home. I still have the CPU and the Shuttle casing somewhere around as I've grown quite fond of the pair.