Thanks for the input, I think that (for this map at least), I am going to side with obsidiian and Torii and clip all the jumps that make sense. jump_apex and jump_finite were the main inspirations for my map, and I agree that the clipping method does look good with dev textures.
BQE, I do share your feeling about invisible walls in general - however in this case I couldn't add a visible indicator without significantly changing the look and feel of the jumps in question, something which I don't really want to do. I'm hoping that as the clips will only serve to smooth out the surface it will not be too frustrating for players. It's not that they would want to use the clipped area anyway, as they are currently nogrenades walls.