PDF files don't stream, so to open one in the first place (either in a browser or on a desktop) it must have been saved to disk. That may be in a browser cache folder, but you can't not save it.
In addition to the physical requirement to have the data saved, the editing/commenting features available in the Acrobat and Adobe Reader browser plugins are intentionally restricted, to prevent users spending time working on a file that's saved in a browser cache only to find it's deleted by the host process when the browser window closes. There are specific exemptions for certain forms workflows and the now-depreciated "browser-based reviews", but the general rule is that to save most types of changes to a PDF file, you have to be viewing it via the desktop application.
Thanks for the response. Maybe I am incorrect, but didn't MS accomplish this for Sharepoint? The ability to open a doc and save it back to the sharepoint farm? or am I completely inaccurate?
Sharepoint does things the way I've described - you can "check out" a document (download it to a local drive), edit it and then check it back in (re-upload it) - but you can't avoid the step where you save a working copy to your own computer.
There are true Cloud-based editors out there, such as Google Docs, Acrobat.com, etc. where you do everything via a browser window and the file itself never leaves the server, but that isn't how Acrobat and Adobe Reader (or MS Office for that matter) operate.