I’ve done this more than a handful of times. As Anadisong mentioned, you’re always kicked from your guild as a side effect of any faction transfer. You just have to be re-invited and re-permission’d after doing it.
Can confirm since one of my guildies swaps between horde and alliance sometimes and every time he needs to be reinvited and everyone teases him about it.
As someone who did this recently, your 7th Legion/Honorbound rep from BFA and Obsidian Warders/Dark Talons rep from DF will both be reset to neutral (if you care about that stuff)