No, you cannot get new Pokemon directly through the e-Reader. In the sense of getting new TYPES (species) of Pokemon, that's just impossible. As for getting another Pokemon in your party/PC that again is probably not possible, though it's not as much an impossibility as the other. It's highly unlikely though that you'll ever be able to GET Pokemon through an e-Reader card (though there is an interesting idea of making an e-Reader program that allows you to custom create any Pokemon, then fake out the cable link trade system and allow you to 'trade' a trashy Pokemon for a 'custom-built' one... And I'd pay for that, but who would MAKE it?!)
No, chances are that they will enable you to get a new Pokemon through the e-Reader using hidden items and events. Much like the EON TICKET and Southern Island. My guess is that the Jirachi event will be based on the WISH TAG, and some event that will become enabled when you get it. Since the Wish Tag is not yet used in the game, and since those little pieces of paper hanging off of Jirachi are called "Wish Tags" according to the Pokemon USA website... Hmmm, doesn't take much math to sum up that total.
Not sure exactly how the event will play out, but my guess is that once you get the Wish Tag through the e-Reader, you'll be able to hunt Jirachi either at random in the wild, or in a certain location on the map. There are also a lot of unused locations in the ROM of the game, and the Wish Tag may activate one of those until now unused locations. Guess we'll find out in a couple weeks, eh?