How about a touch system on the map.

First touch to the screen causes a small red dot over the area with a pulsing line that connects back to current location. (The pulse shows direction much like most update bars in Mac OS, I'll have to grab a visual to show better my idea).

This way user can see if they've clicked the wrong sector/square as well as see distance and direction of travel.

Furthermore you could have it that the first touch is red, the second touch is yellow. Second touch sets a waypoint.

I understand the devs don't want to automate units too much. So perhaps limit the amount of way points a ship can be set. Pehaps just 1, so you can do something like set probes for a little while longer. Perhaps make it a skill to level up? This will force an interesting trade off if someone wants a more automated system.

Third touch sets the dot to blue and user can now accept the decision by pressing check or cancel.

Regardless of waypoints this idea would certainly help as a feature. It would save me from constantly sending probes into the wrong square/line.