Upon some tests, the jumpbot riot stops halberds COMPLETELY in their tracks, being (by far) the best counter for their cost, invalidating the halberd runby completely.
Of course, it is always cheaper to try and make a wall in weird spots than let weird halberds come by unnoticed.
Pyros seem to fair the best against direct attack on halberds, as they both soften halberds up and deal massive damage.
Overall, as it was well-stated, the biggest problem with halberds is stopping them before they destroy the entire base. The rest is clean-up.
The question is answered.
Bonus note: Jumpbots seem to hard-counter hovercraft in general, it's worth considering