There is no solution as you would want it I am afraid. You can do workarounds, like setting the rally point to where the phase line from C to D begins and then manually telling the ships to jump to D (or generally, setting the best/longest straight safe route and correcting it at the end). Other than than, you can only build/use a frig factory somewhere else or make phase stabilizers if you are Vasari.
Maybe building the frig factory immediately next to the phase line from A to C will make your ships choose this route over the other.

It sure would be nice if we were able to put a red cross stamp on planets to mark them as hazardous, which would tell all fleets to omit this planet when looking for a route somewhere (unless directly ordered).
I would definately Red Cross all pirate bases and neutral colonies. I hate losing my scouts en masse when they try to fly through these.

Ya I don't know if that works with rally points - if it doesn't that would be a nice feature HINT HINT

Oh bummer

You've have to just pool them up and move em at once