There is no problem with doing that. Of course, you wouldn't want to go from "patched" console to "unpatched" OFW, but installing OFW/HFW will get you to the clean state where you started. In case that you got stuck on the old method, I would recommend updating to HFW 4.90 and following the video mentioned above.
This happens from time to time. As long as it isn't in the process of "Installing, do not turn off the PS3!", there isn't any risk of bricking. People at Sony actually did a great job of making it as safe as possible. Whether you need to unplug it... I would personally give it ~30 minutes to do whatever it needs to do, and if nothing changes, just unplug it.
Also, if possible, try using a different USB flash drive on the next attempt.