They just hosted most of the code on a server. It's kind of like the "native" iOS apps that just use a webview component to display a web app. Sticking with IE6 just means you have all the hassle of a native app (like needing to make sure IE6 gets installed and stays installed on every machine) with none of the benefits.
At the time, IE6 WAS installed on every machine and using it as a platform for internal apps was VASTLY easier than deploying client/server apps that needed a powerbuilder or some such runtime on each desktop.
It sounds like that's exactly what they did,
They just hosted most of the code on a server. It's kind of like the "native" iOS apps that just use a webview component to display a web app. Sticking with IE6 just means you have all the hassle of a native app (like needing to make sure IE6 gets installed and stays installed on every machine) with none of the benefits.