After consulting with an esteemed colleague today he alerted me to the Safari Developer Toolkit, and how this can be connected to UIWebViews in the iOS Simulator for console output (and debugging!).
Steps:
Open Safari Preferences -> "Advanced" tab -> enable checkbox "Show Develop menu in menu bar"
Start app with UIWebView in iOS Simulator
Safari -> Develop -> i(Pad/Pod) Simulator -> [the name of your UIWebView file]
You can now drop complex (in my case, flot) Javascript and other stuff into UIWebViews and debug at will.
EDIT: As pointed out by @Joshua J McKinnon this strategy also works when debugging UIWebViews on a device. Simply enable Web Inspector on your device settings: Settings->Safari->Advanced->Web Inspector (cheers @Jeremy Wiebe)