Not so much good or not good, but quite possibly unnecessary.
I think we can all agree that shooting an arrow from a (presumably) rocking in-motion position is harder than doing it from a stable position, but then we can ask. 1) Is it enough harder that a penalty is warrented? 2) Is the character capable of compensating for the rocking enough to make it moot (what I call "the expected competency conundrum"; 3) Does the advantage of height mitigate the motion? (I would argue yes: there must be a reason that people chose to shoot "from the tops" historically, but even having researched it, I'm not entirely sure what all those reasons might be).
So, I mean, you made a ruling, which is fine, just, and allowed. Is it a good, reasonable, or just ruling? It's up for debate. I can tell you: I would not have ruled that way.
But I'm NOT saying that you were wrong to do so. (This is often confused on these boards, on both sides of anything.)