There's an easy solution to this - don't activate direct to your destination while still on the ground. Get it entered, but then wait until after takeoff and initial climb to activate it. Voila, now you've only done it once and aren't "cheating".
That's only said a little in jest. The idea, usually barring something like a precision flight competition, isn't to go direct from your parking spot to the destination airport. It's to go to the destination airport via the shortest route, which would by default include climb and initial maneuvering. When I teach Private students (which is not often), I don't even have them plot a course line from airport to airport, because it's irrelevant. Rather, I have them plot the course starting at a nearby checkpoint they are likely to fly over once their climb is complete. Why make a plan which you know is 100% going to not work the instant you move from the parking spot? Same idea applies to GPS direct. Put it in there for reference, with the expectation that you will do re-do it after initial climb. It's not cheating, it's how it should be done.