I think the solution could be to check if V_Path is straight up or down (that seems to be the problem), and if it is aligned vertically then do not rotate the vehicle and let it contiue in straight line untill the the rotated destination (V_Path) is not vertically aligned anymore. Not sure if that could be the solution, just a random thought...
Yes, that sounds ideal. V_Path is (in theory, anyway) straight up or down when the destination is directly opposite the vehicle's position (that is, if the vehicle was to tunnel straight down through the planet it'd surface at its destination). As such, in this case, there is no "shortest path" to the destination, and the vehicle can move in any direction it wants (ideally, I guess, continue in the direction it was already heading). (
EDIT: I see your edit, but I still think this is the ideal solution, once we get that green line to stop wobbling so much

)
The way the green line wobbles, it appears that the alignToVec function isn't very accurate, and I think this is the problem:
Modified version of your function I am currently using:...
That's actually how I originally wrote it, only to find that rounding errors caused a lot of trouble. This is because vec_length(rotAxis) can get quite small. I added in that multiplication so that the final angle always
undershoots the rotation, so it still looks smooth as you approach the appropriate orientation; without it, the final result can overshoot, resulting in weird behaviour (which could well be the cause of that wobbly V_Path).
So I recommend uncommenting that extra bit and seeing if multiple alignToVec(...)s reduce the problem.
I hope that's useful (and correct!).