They're tweeting that they'll delete their Instagram accounts because of the acquisition.
The fear is that in addition to the company, Facebook has acquired all of that location-tagged photo data from Instagram's users and may use it to target ads at them. Neither company has commented publicly about whether the data will, in fact, be used by Facebook in this way.
If you're in the camp that's deleting its Instagram accounts regardless (which you can do through this link), you don't have to give up your photo library in the process. Here are some ways to save it:
Instaport: In two steps, this service downloads your entire library onto a single zip file.
Copygram: The primary function of Copygram is to provide a web interface for Instagram. It also allows you to download your library and pictures from other users' feeds.
Instagrid: This web interface for Instagram doesn’t let you download your library. It does, however, provide access to your favorite users’ photo streams without requiring you to have the Instagram app. You can subscribe to emailed updates from specific feeds (provided they use the service) or a weekly digest of both popular and “undiscovered” Instagram users.
InstaDesk: While InstaDesk is certainly more fun to use with an Instagram account, it's also a good tool for saving your favorite photos before shutting one down. Even if you've ignored its sync feature up until this point, the $4.99 Mac client makes it easy to download Instagram photos.
SocialFolders: This service touts itself as a "Dropbox for Social Media." In addition to your Instagram account, it will back up your Twitter, SmugMug, Facebook, Flickr, Picassa, Google Docs and YouTube profiles -- so next time you want to delete an account, you'll be prepared.
Keep in mind that some of these services are running slow today, apparently due to an overloaded Instagram API or increased traffic on the sites themselves.