Is there any way to check if a URL scheme is currently registered on the phone... with javascript?
Not seamlessly. But there is a way similar to checking if a pop-up was blocked or not.
When you try a URL scheme which is not supported, Safari will warn the user that it doesn't know what to do with it and stay on the same page.
So if you gave your app-call some time to activate, say 300 ms, and then do something else to respond to the non-existence of the scheme.
It's not the prettiest but it works:
function startIThrown(){
document.location = 'ithrown://restart';
setTimeout(function(){
if(confirm('You do not seem to have iThrown installed, do you want to go download it now?')){
document.location = 'http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=293049283&mt=8&uo=6';
}
}, 300);
}
<a href="#" onclick="startIThrown()">Restart iThrown</a>