This is a reasonable question, though tangential to the original article so you're going to find some criticism among those who miss the nuance. I assume you're not making an argument against climate change being an issue, but asking a related question.
By my understanding the natural cycles in climate that you refer to occur in hundreds of thousands of years time scales, and we know a reasonable amount about them with regards to Milankovitch cycles, but there are other factors like solar cycles that can influence climate that still add some uncertainty. How we might go about cooling the earth or whether we even need to in response to a natural warming cycle may be entirely different to our response now, because of this difference in time scales.
Over hundreds of thousands of years, populated areas that would be affected by rising sea levels are likely to be rebuilt many times. Any increase in sea levels is likely to be accounted for in this naturally, and such issues may never arise in large enough cities. Other places that cannot be built up will likely be abandoned and eroded by the sea over time, with abandonment not unusual for localities that are deemed no longer habitable or economically feasible.
As far as cooling the earth if it is necessary, I expect that we will be looking toward space exploration to help us here. Any science toward terraforming other planets will help, so colonizing Mars may be a useful near-term goal. I assume technologies to control the heat retained by the planet would be important, either by reflecting solar radiation before it reaches our atmosphere, or by controlling the levels of greenhouse gases. If we had the technology now, we could essentially do the same thing, however we don't, and won't.
The difference in time scale involved here is the main point. Man-made climate change is occuring on a time scale that our current technology has no ability to counter directly, and this has huge ramifications on short time scales economically, and for the quality of life for coming generations. Natural climate change occurs on a much longer time scale, so any economic impacts are likely to be amortized across the duration of the change and will probably end up in the noise, with technology likely to be able to keep up if we are intelligent about managing our own contributions.