We had to reboot a server in the middle of a production day due to 99% iowait (lots of processes in deep sleep waiting for disk iops). That's never happened to us before.

It had been 363 days since the last fsck, so it started automatically on reboot. It hung at 4.8% on a 2TB LVM2 volume for about an hour. I killed the fsck and rebooted the server. The second time, it went past that point and is currently at about 62%.

First, what causes e2fsck to hang like that? Second, is there any danger in killing e2fsck, rebooting, and starting it again?

Can you post your dmesg? I just want to see if any errors came up either during when it hung or when you killed it.

It can hung due to many reasons, one being having a lot of bad inodes, and it is just taking a long to time to recover them. I advise next time you give it longer than an hour to see what it does, along with running it in verbose mode for better output and to see if anything is occuring during the "hang time" so to speak.