Sure, the system is quarantined, even though its probably just the planet, but the infection happens AFTER Gabriel is revealed. Its not like the Lyrans are going to stop watching over the system and the Ruins because the WoB poisoned one of the planets.
They're not going to suddenly forget about the Ruins in the system.
Maybe if the WoB had poisoned the planet before the Ruins had been discovered, I could see it as an attempt at hiding the traffic in the system, but it didn't happen that way.