I installed Ubuntu 13.10 a few days ago, and had to use boot-repair to get dual boot (with Windows 8.1 on a computer with UEFI) working properly, setting up GRUB and all that. But I kind of don't like Unity, and would like to use Xfce instead. I'm debating being lazy and just using xubuntu-desktop versus doing a fresh install of Xubuntu, but in the event that I do a fresh install, would I have to run boot-repair once more or would GRUB and the booting process remain intact and be able to boot Xubuntu immediately?
Yes, you will likely have to run boot repair again to be able to boot into windows.
Installing the xbutnutu-destop package is a better option if you want to avoid this.
Once you are satisfied that you don't ever want to run gnome or unity again you can remove them per this answer, but be careful not to remove X.