In iOS 4.0, your application will be placed in the background image if another application comes to the fore and there are enough resources to keep your application in the background. You can send the Safari URL or another application registered for the handler and hope that there will be enough memory (etc.) so that the OS puts your application in the background after starting Safari (or any application that processes the URL the address). If you're lucky (which usually happens quite often), you programmatically send your application to the background.
Of course, whether your application will run in the background or simply paused depends on other things (which you must register in iOS 4.x for).