Firstly, I have never thought of such an approach for stellar navigation. I like it. If you have time, you could try to make it less linear, but not necessarily ovular or circular- like a topographical map. As for the idea of using color to distinguish elevations, just be sure to use colors not also shown in the stars presented. You can have red stars and darker purple lines to indicate higher or lower elevations (per the galactic plane), so long as the redness of that line is not too similar to the red star. That sort of thing.

If you intend to have navigational lines between systems, though, I wonder if shadows on them would help to prevent confusion between elevations and course routes (possibly, also, dotted lines, where the negative elevation doesn't interfere). I can't say for sure how well any of this would work, since I draw things by hand to begin with, at least.

I hope this helps.