Photo Stream should not have done this; and I doubt it did. More likely something else happened and turning on Photo Stream was just a coincidence.
I have Photo Stream working with Aperture without a problem, though I suggest you go into Preferences > Photo Stream and turn off automatic uploads (unless you want every Aperture import to show up on the iPhone and iPad). iPhotos should work similarly. I can't check because I'm a version behind.
On you iPad be sure you aren't just looking at Photos Stream instead of your Camera Roll. It's easy to get confused about what you are looking at (All Photos, Camera Roll, Photo Stream, or albums.
If it's your synced Albums that have disappeared try a restart or reset and see if that helps. Otherwise you'll need to connect the iPad to your computer and check out what happened to your photo sync settings.
iOS and iPod: Syncing photos using iTunes
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When you have problems with an app it's a good idea to clear it from RAM.
Close/Clear the app: With the problem app closed, double tap on the Home button to get the multitask bar. Tap and hold on any icon in the bar until they jiggle, then tap the minus sign on the problem app. This will remove it from RAM and insure a clean start the next time you launch the app.
If that does not work try a restart,
Restart: Hold down the power button until the power off slider appears. Slide it off. When the iPad finishes shutting down, hold down the power button again until the Apple logo appears. Apple recommends you restart the iPad at least once a month.
and then a reset if that does not work.
Reset: Hold down the power and home buttons until the Apple logo appears. The iPad will reboot. This usually takes a bit longer than a restart.
