Fedora :: Really Bad Idea To Multi-Tasking During Update?

It seem like a good idea to leave the computer along when it is updating. Because if for some reason I still using the computer, it might interrupt the updating process.(e.g. update manager freeze, or corrupt some file) I remember I run into this problem quite a few times back in FC6, but did not have problem on F10 and F11(merging from preview?) until the day before yesterday. I was tried to downloading a relative large file updating system and running 2 folding at home in the terminal at the same time (ram usage at the time was around 300+/512). Then disaster strike. The hard drive spin like crazy with large cpu I/O pending(or wait time?). The problem reoccur during the boot up and login after the update.

And this is the message continue recorded in the (F11) log:
Oct 17 11:52:22 localhost kernel: ata1.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0
Oct 17 11:52:22 localhost kernel: ata1.00: BMDMA stat 0x24
Oct 17 11:52:22 localhost kernel: ata1.00: cmd c8/00:08:22:9c:57/00:00:00:00:00/e6 tag 0 dma 4096 in
Oct 17 11:52:22 localhost kernel: res 51/40:07:23:9c:57/00:00:00:00:00/e6 Emask 0x9 (media error)
Oct 17 11:52:22 localhost kernel: ata1.00: status: { DRDY ERR }
Oct 17 11:52:22 localhost kernel: ata1.00: error: { UNC }
Oct 17 11:52:22 localhost kernel: ata1.00: configured for UDMA/100
Oct 17 11:52:22 localhost kernel: ata1: EH complete

I saw this message in F10 before, and had been told it might have something to do with the kernel. But I suspect the problem is source from corrupted file rather than kernel this time around, since back then the problem will go away after a successful file system check. Unfortunately, it does not work this time. So I have no choice to reinstall the system. Therefore, I am thinking if it is really a bad ideal to let the computer muti-tasking during the update? Because it may rise the possibility of update failure or system files corruption. I really do not like LVM, is there a way to get around it? The installer from live usb does not allow me to customize partition during the installing....