You can't force-stop the stock keyboard (only if you root, and even then, I suggest you don't. If anything happens you're left without a stock keyboard to type in your password at boot).
Do you get the pop-up randomly or when you start typing on a text field? Is SwiftKey selected as your default keyboard? The selection icon at the bottom of the screen and on the notification bar when you're typing won't ever go away, but if you have a keyboard selected as a default, the selection pop-up shouldn't just, well, pop up on its own, just if you select the Select Keyboard button or notification.
Do you use SideSync? I had a similar issue when I used it but all it did was go back to setting the stock Samsung keyboard as the default, but never random pop ups (and this was on an S7... I haven't had that issue on the 8).