Then maybe treat ponds like shallow water. Slow down the troops but do not submerge them.
What do you think?
In QB.csv change Unit Can't Halt entry for IDS_MAP_POND (Greyscale 12) to 1. By default it is set to 0 for the QB map but in all other maps that come with the game, POND is set to 1 for "Unit Can't Halt". This will make it impossible for units to sit in the water and fire. They will still occasionally move through it (especially when retreating) but on the whole they try and avoid it and it solved the problem for me.
This is a good alternative for now. No need for a shallower pond as long as the units don't stop, but it would look more realistic.