Exact same issue on iMac running 10.7.2. Tried three times to update to Safari 5.1.2 and iTunes 10.5.3. Every single time I would get stuck at "Running package scripts" - I even left it overnight on the third try to no avail. Each time I would just do the hard shut down (holding down the power button for a few seconds), and then start the iMac back up and it would resume to normal operation (yet with no updates).
Then, just now, I turned off Time Machine in the system preferences, ejected/unmounted my 2 TB external HD that is the Time Machine backup, I unplugged the USB cable from the back of the iMac, then re-ran Software Update to re-download these two updates and attempt the re-install.
Machine rebooted, ran the update in five minutes or so, then I logged back into my user account, plugged my USB external HD back in, turned Time Machine back on, re-selected the disk, and I'm up and running!
Glad to know I could get the update done unplugging the external drive. But such a hassle getting there.