I haven't tested this but it should work.
Remove references to tower meshes in the desc_engines.txt file and replace them with a new model you've created. it could be a wooden wall to protect archers from missiles, or anything relevent to your period.
Adjust the stats for your new engine and make the docking distance something large, around 30?
You might want to remove the missile ability of the tower also.
Code:
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
type siege_tower
culture all
class tower
variant small
projectile arrow
engine_model_group normal
engine_skeleton siege_tower
engine_collision data/models_engine/small_tower_very_low_lod.CAS
engine_model data/models_engine/small_tower_model.CAS, 100
engine_model data/models_engine/small_tower_med_lod.CAS, 200
engine_model data/models_engine/small_tower_low_lod.CAS, 400
engine_model data/models_engine/small_tower_very_low_lod.CAS, max
engine_platforms data/models_engine/small_tower_info.CAS
engine_model_group dying
engine_skeleton siege_tower_dying
engine_model data/models_engine/small_tower_dying_model.CAS, max
engine_platforms none
engine_model_group dead
engine_model data/models_engine/small_tower_dying_dead.CAS, max
engine_platforms none
engine_shadow none
engine_radius 4
engine_length 7.0
engine_width 7.0
engine_height 23
engine_mass 40
engine_dock_dist 6.6
engine_mob_dist 8.0
engine_flammable true
engine_ignition 0.20
fire_effect engine_fire_siege_set
obstacle_shape rectangle
obstacle_x_radius 4.5
obstacle_y_radius 4.5
engine_spo physical_obstacle
engine_push_point -3.5 4.5
engine_push_point -1.75 4.5
engine_push_point 0.0 4.5
engine_push_point 1.75 4.5
engine_push_point 3.5 4.5
engine_push_point -3.5 5.5
engine_push_point -1.75 5.5
engine_push_point 0.0 5.5
engine_push_point 1.75 5.5
engine_push_point 3.5 5.5
engine_health 130
;engine_weapon ballista
;engine_armour siege tower
attack_stat 8, 2, arrow, 100, 100, missile, archery, piercing
attack_stat_attr ap
arrow_generator 2 21.8 3.3
aim_dir 0.0 0.0 1.0
aim_arc 1.0
fire_interval 1.5
arrow_generator 1 21.8 3.3
aim_dir 0.0 0.0 1.0
aim_arc 1.0
fire_interval 1.5
arrow_generator 0 21.8 3.3
aim_dir 0.0 0.0 1.0
aim_arc 1.0
fire_interval 1.5
arrow_generator -1 21.8 3.3
aim_dir 0.0 0.0 1.0
aim_arc 1.0
fire_interval 1.5
arrow_generator -2 21.8 3.3
aim_dir 0.0 0.0 1.0
aim_arc 1.0
fire_interval 1.5
missile_model data/models_engine/Bolt_high.CAS, 20.0
missile_model data/models_engine/Bolt_high.CAS, 40.0
missile_model data/models_engine/Bolt_high.CAS, max
missile_pos 0.0 22 0.0
missile_radius 1
missile_height 2.5
missile_mass 3
R