They didn't have a way to do it without major disruption to the system, hence the final last ditch effort of taking over SOP once they began bringing online such systems after S3 and using the nuke and REX's railgun to take out JD (which they'd only just found out about was hiding as orbital debris).The Kernel wrote:
That's circular logic. You are saying that because they did what they did it MUST have been the only way to achieve their goal which doesn't make any sense. Once they had physical control of GW (which they did back in MGS2) they should have been able to knock out the AI cluster with zero issues.
No doubt they could gave tried to take out the system using just GW that way, but without Sunny using Emma's code and her experience from within the Patriot network, they could have essentially left the world in anarchy. It was fortunate that they had a worm that intricately knew how to disconnect the AIs from the systems they controlled without harming their environment, otherwise they had just the nuke it option on the table. With only Zero left to really sculpt a world in The Boss' ideology, everyone else was on the outside up until MGS2 with George Sears/Solidus going rogue, albeit, failing as part of S3.
It's not like they didn't try all of this before anyway, since MGS2 had an attempt to take out the network which failed, even if it gave them a chance to salvage the autistic GW and use it later to build up again and try a better route. Liquid acquiring PMCs and the like was for the eventuality of taking down JD et al and then asserting authority without civil war erupting globally.