A two-handed overhead thrust for polearms is already in the native .brf files. You can change the action.txt file to use it. The problem is that doing so replaces the overhead attack animation for all weapon that use the current polearm overhead animation. This would mean that weapons like the long maul and poleaxes would have a high thrust instead of the downward overhead slash. One possible solution would be to make all of the "thrust first" polearms (long spear, pike, awlpike, etc.) weapon use the modified polearm overhead thrust and make all of the slashing/crushing polearms use the current two-handed weapon overhead attack. However, the use of the two-handed weapon animation would increase the range of the overhead attack of many already powerful polearms by ~30 cm.
Using 2H overhead animation for polearms looks reasonable. The main difference is which hand is infront of the other (right forward in 2H, left in poles). Polearms are a kind of weapon in which the grip is often and rapidly changed and this is neither unrealistic nor awkward looking.
In terms of game balance, if the reach is excessive (I seriously doubt it), these weapons can take a small damage nerf. The current situation in which a 2H sword reaches as far as the swiss halberd is not exactly balanced either. The long Maul whose main attack is the overhead for the crushes can simply be shortened (also the 3D mesh).
The other problem is that if the overhead damage becomes pierce, it will be pierce for side swings as well. Not so good for implementing on the likes of the war spear, so 4-way polearms cannot have a second pierce attack. Will really help the forks, ashwood/awl pikes, long spear and even the boar spear may become more attractive as a 2-thrust spear.