Could you be more specific, because I was definitely under the impression that the original quote was correct.
Where are imaginary numbers required for the undamped mass-spring system? Because a lot of "complex" equations are using complex e^ simply as an alternative to trigonometric functions (for aesthetics or convenience), where there's nothing inherently imaginary whatsoever. The same as much of signal processing.
I'm less familiar with using complex numbers in linear algebra, but I know that when I studied it in college we never touched them, so I don't understand how we'd lose most of linear algebra?
But I think the point the article is making is that, except for QM, there are no physical instantiations of complex/imaginary values. Rational numbers physically "exist" as a fraction of a distance between two points; real numbers "exist" as actual geometric proportions, and negative numbers "exist" as an opposite direction. But complex/imaginary numbers are just intermediary tools for solving equations (or conveniences to replace trigonometric functions), they don't correspond to anything physical (except, it seems, in QM).