From the sound of the description the original CTO authored code was cobbled together and its replacement was properly engineered (for some value of properly).
And I'm sure if you said that to the CTO they wouldn't take offence and would react in a rational, measured way. Actually, I've worked with managers that would react OK to that, and ones that definitely wouldn't, but I wouldn't tell any of them their work wasn't "properly engineered". Stick to the objective facts: this version runs much faster (no need to even mention the 'several orders of magnitude' factor unless they really want to know).
Of course, but from the time invested, it would seem the other way around. It's often painful to accept that you wasted a lot of time and that it's better to start over (which is of course the entire point of the article), and even more so if the new hire has already done that and thrown the CTO's code away.
Ultimately it's a question of ego. Does the CTO welcome the new hire who knows more about this than he does, or does he insist he knows better? Does he feel threatened or slighted?
