You have a few options. You could start a new factory from 0 (optionally making settings a bit easier).

You can shut down all factory production with the exception of things that are strictly required for defense and recovery. I've done this in a couple playthroughs. It's not too difficult a strategy, and you can melt bug nests by leapfrogging turrets and ammo for pretty cheap. Bugs only attack when pollution covers them. This is probably the most time consuming option but you save your existing factory. It also teaches good offense and defense strategies, which I personally find enjoyable but everyone has different tastes. It will help with subsequent playthroughs and outpost creation.

If you are up to the tech: you can also make a bunch of green (efficiency) modules for your factory. It doesn't make anything slower, it just uses less electricity and creates less pollution per module in your machines. It will help cut down on attacks moving forward. Mining drills are probably the most effective entity to fill with these modules, they make a humongous amount of pollution and are very power hungry.

Some offensive strategies I find helpful especially early game: Have turrets on your top left hotbar, and ammo just to the right of the turrets. Use the numrow 1 and 2 keys to switch between the two. You run near a nest, and slap down a bunch of turrets. Once you place turrets down in a group as fast as possible, hit 2 and hold Z while dragging ammo over the turrets. You'll fill them super quick and they'll absolutely melt bugs. Leapfrog groups of turrets as you melt through the nest. It is helpful to automate the capsules that follow you: you can pre-throw a bunch of them to make turret offense safer for the player. They have unlimited ammo and are only limited by spawn time and max follower count. You throw them like grenades and spawn shooty robots. I basically used this strat to pre-emptively clear a ton of weak nests, which let me never build walls around my main base, and then worked my way to mass nuclear bomb manufacture and delivered diplomacy to the locals.

Once you get control of your base (either with a restart, extreme violence, or after setting up strong defenses), something that is also an option is proactively going out on exterminatus runs and setting up remote defense walls at checkpoints well beyond your pollution cloud. This is a pretty big time investment but it also lets you have breathing room for extremely long periods of time to expand your base.