The problem is that to maintain total control, you have to have players available nearly 24 hours a day who are willing to put in the legwork to find every wormhole in and out of the system as the game auto-generates them. This is tedious work, and so it's basically impractical to have that level of control.
The attackers utilized small gaps in the otherwise extensive hand-monitoring of wormholes that HK undertook to move freighters full of ships through wormholes. Then the player controlling that freighter logged out of their account, and when a player logs out, the ship they're controlling warps off "to infinity" automatically and is completely safe.
For HK to protect against this attack completely, they'd have to have ships on patrol at all times AND those ships would have to be sufficiently equipped to catch and kill a freighter before its player can get logged off and the freighter auto-escapes. It's a tall order.
... and it's worth noting that even given those constraints, this attack was basically thought to be impossible. The Initiative took a year to make this work with enough freighters to shift the balance of power.