The short answer, I’m afraid, is no. Sorry!
The long answer explains why:
When we control Keynote on the Macintosh, we use our free Presentation Manager app to act as a sort of liaison between Presentation Remote (on the iPhone/iPod touch), and Keynote. This isn’t possible on the iPad, as only one application can be running at once — you would have to quit Presentation Manager in order to start Keynote.
Now, later in the year, the iPad is scheduled to get multitasking. Will this help? After all, we’d be able to run an iPad Presentation Manager side-by-side with Keynote, then.
Unfortunately, applications on the iPad are “sandboxed”, meaning that there’s a sort of protective barrier around each application. This is, in many ways, a good thing — it helps stop badly-written applications from causing trouble with other apps, and is also one of the reasons that iPad users don’t have to worry about viruses in the way that you might on some other systems.
But it also means that, even if we could get Presentation Manager and Keynote running on the same iPad, that barrier would prevent Presentation Manager from sending commands to Keynote, or finding out the sort of information it needs to do its job —finding out what the notes are for each slide, for instance, or which slide is currently being shown.
Of course, we’ll keep an eye out for changes to this in future — but please don’t hold your breath; the application sandbox seems like one of those fundamental decisions that defines the way iPad works, something that Apple is unlikely to change their minds about.