That's a ridiculous statement. Web UIs are pretty awful, unpredictable, confusing and non-standard compared to desktop ones. Not only that but they're hard to develop, you have to jump through hoops of CSS hacks to make things behave in a sort-of-desktop-like fashion.
There are many high quality graphing libraries available on desktop apps (Qwt, QCustomPlot, DevExpress to name a few I've worked with).
The training thing you talk about is true though, if your team has more experience on the web, then retraining them is wasted effort I suppose. Depends on your idea of quality result though.