Helgen is more accessible to the frontier, being it is on the road to another province. Travel south from Helgen past Fort Nuegard and you are in another province, well you are over the mountains that protect Falkreath. You have to go past Helgen to get to Falkreath if you were to invade, so it makes sense that Helgen is the fortified town.
Also, Helgen is closer to the border than Falkreath is. Not by much, but is closer as the crow flies. However, Falkreath is much farther away as the army marches.
http://images.wikia.com/elderscrolls/images/b/b7/SkyrimMap.jpg
This map makes Falkreath look closer, by a little bit. Not that it matters all that much. It also shows a road going over the mountains. The game doesn't show everything that is 'actually' there according to lore (or common sense, in this case).
It's a weird border to fortify in any case, as the Imperials would never build walls against Cyrodiil. Better to drop the whole line of reasoning. Much more likely is Falkreath losing the privilege to have walls, which historically speaking was a marker of independence.