Would it be possible to have the game prioritise units their pathing to walk through the gate, unless the unit has been selected to climb a ladder? I believe this was the case for both Warhammer I & II, as well as historical titles that featured the same wall climbing gameplay (Empire, Napoleon, etc.). 

I think because the game is trying to work out the shortest distance inside, and it considers the gate blocked when a unit is walking through, it really disrupts/splits entities different directions, whereas for some factions you would prefer most of your units to charge through the gate.