You should check out Parse (www.parse.com). You can both send push notifications and write server side scripts using JavaScript using what they call Cloud Code. It's pretty awesome.
Although I suppose you could get around the multi-push-certificate restriction with multiple Parse accounts. If you had two iOS apps, then you'd be making two web requests out to Parse. Although I do this now with UrbanAirship so there would not really be a difference. Interesting.