I don't think it's fair to compare hyperthyroidism to a heart murmur. Hyperthyroidism will definitely affect a cat's quality of life if left untreated (having thyroid disease myself, I know!!!).
The heart murmur, on the other hand, depending on how serious it is, may shorten the cat's life as the heart may fail at any time. But if he's an indoor cat, and not overly active to the point activity would cause him problems, his quality of life should be fine.
It's my understanding that it can be controlled rather easily with medication, but a lot of animals don't like taking medicines. You wont know how your cat is until you try to do it. If he doesn't like it, and he's fine otherwise, I'm more along your initial thoughts of why make his life longer but worse? I'd rather he have a happy, stress free life, no matter how long it is, rather than him be uncomfortable for a longer period of time. Again, it depends on how bad it is and what symptoms you can expect. If it's something that's going to affect his quality of life, I'd treat him. If there's the potential his life may be shortened, but fine, I probably wouldn't do it. Going quickly due to a heart attack is a lot different than slowly suffering for a long time because of thyroid disease.