I usually build Monasteries for the culture, not for the science. Thus, I'm never upset that my +85% beakers goes down to +75%. I
am upset that I lose an extremely cheap way to expand the cultural radius of newly built cities and shrink the cultural borders of my opponents. Also, although SM reveals Oil, that resource is useless until you get Combustion, and then you're just trading whales for oil instead of actually gaining anything. All told, it's a pretty bad deal.
I also avoid researching Calendar for the same reason. Unless spices, sugar, dye, banana, incense, and silk are virtually the only resources in my territory, I'd rather keep my Stonehenge.
I don't care how you attempt to rationalize this idiocy. Any game in which you're actually better-off without a technology than with it is an example of bad game design.
EDIT: Apparently, BtS delayed Stonehenge's obsolescence until Astronomy, so if you're playing BtS, you can have your Stonehenge AND your spices. Pretty cool.
EDIT #2: Once the Scientific Method comes along, wouldn't the monks switch to it instead of dropping out of science altogether? As someone said earlier, Gregor Mendel is a perfect example of this.