FWIW, it's clear that you _did_ mislead Jacques.
Whether the assumptions he made were valid or not (and frankly, based on the content of your homepage, it's hard not to have sympathy for his point of view), he clearly expected you guys would do a better job hosting Wordpress that he could do himself on his own Linode VPS. He also clearly expected that if there were problems, your "Expert Wordpress Support" would provide the solutions. Instead he found your support guys effectively saying "we don't know how to do that" and flicking him on to WebSiteMovers, who _also_ end up saying "we don't know how to do that" and charging him $500 for failing.
So I think you did let Jacques down, and I think he has every reason to feel missled.
You should probably acknowledge, at least prominently enough that anyone researching your service with a view to becoming a paying customer will find it, that there are possible pathological cases and configurations which WPEngine's technology/infrastructure/service will not solve. If you don't want to feature this on the homepage (and I can understand you not wanting too), I'd suggest a note near the top of the Disallowed Plugins page - and probably re-wording that page to make clear that avoiding everything on the "complete list" of disallowed plugins doesn't guarantee a successful deployment, and also that it's possible for themes with certain code patterns in them to cause a WPEngine deployment to fail to perform as advertised.
Secondly (and I suspect you've already got this one in hand), you need to train your support staff to recognise more quickly installations with pathological performance things going on, and apologise and extricate yourselves and inform the customer as early in the process as practical. I don't know what the tone/implication in Seans message about the ~188k row sort was, but from reading your defence here I can't help but think there was at least a bit of "you're doing it wrong!" - which even when it's true, it's not the wording you want to feed an unhappy customer.
(Note: this is written as a happy WPE user, with some curiosity about exactly what went wrong, and why some guy with a Linode VPS can, in some cases, keep a Wordpress site up better then WPE. I'm suspecting he's got define('WP_MEMORY_LIMIT', '2048M'); or something similar covering up some quickly hacked together "it works for me" not-very-well-though-out-code - which you can get away with on your own hardware/VPS, but not generally on shared hosting...)