I mostly agree with the sentiment. Slow, incremental changes, whether to code or even a website's style. Mostly. But sometimes you run across code so malign, so neglected, so undocumented, uncommented, twitchy, troublesome, inexplicable, that the risks of the Second System Effect are worth it.
Really, I think the crucial point comes when your system is a kind of obelisk. You tiptoe around it, make offerings, but you don't know how to appease its wrath. It's like the weather.
Then it is time.