There's no Kingdom of Prussia without the Knights, but there could have been a kingdom of Prussia without Brandenburg. At least, I see it that way. But it's not my area of expertise, so I accept your judgement.
Well, if you're going with alternate history there's no kingdom named Prussia without the knights' secularization, but the core of the historical kingdom is still there, and just happens to be named the Electorate of Brandenburg, and could play the same role it did historically.
If you take Brandenburg off the map--say, divvy it up after the 30 Years' War--anything that was named Prussia (kingdom or not) is a minor state on the Baltic that has nothing to do the Prussia that unified Germany. It probably gets gobbled up by Sobieski.