Aligning the Java release schedules for OS X and basically all other platforms would be fantastic. Rather than some kind of deprecation, this actually makes OS X a first-class citizen in the Java ecosystem.
I think if Oracle quickly steps up to the plate and promises to fill Apple's shoes, this could be a good thing. Otherwise, this could very well be another downside to Oracle gobbling up Sun.
Straight from the source means ... ta-da! "Optionally installed". Therefore, no Java-based apps in the Mac App Store.
Bad for Java app developers on the Mac - Apple's app store is likely to be a very good channel for sales - unless Oracle step up to the plate with a (cross-platform) app store. But good luck with that - it won't be so visible, cross-platform apps are generally dodgy, and it doesn't have Steve Job's magic pixie dust.
I find it hard to see the issue, if you are using Java to build an app you are developing a Java app not an OSX app. You are targeting a different run-time than a standard OSX app. To me it is no different than Apple saying you can't sell an Adobe Air app in the app store. or a C# app running on Mono. I see a very valid reason why Apple would instate such a policy. Even though in the past Apple supplied the run-time for Java it still did not make it OSX it was just a very well tailored JRE for OSX, you still write Java apps and not OSX apps if you target the JRE.
All the jars and whatnot, I don't think that's the model Apple has in mind for things distributed via the App Store.