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If you are an anti-alien faction, you probably want to hunt down and assassinate the alien agents ASAP. Try to kill off enemy ships before they can crash-land reinforcements. (This will obviously make the aliens mad at you, so expect consequences.)
All alien agents can seed xenoflora, their transports arriving will seed xenoflora and the Servants get an org that allows one of their councillors to seed xenoflora. Not sure about the existence of any others. Events can also seed xenoflora.
If you actually eliminate all alien agents and stop others from arriving then you will be able to prevent almost all xenoflora from existing by repeat actions from armies, councillors and gunships.
Finally there's a bunch of technologies that will boost your effectiveness while clearing xenoflora, which means that you will focus down the really bad stuff to something more manageable in fewer order cycles.
My current game has gone very slowly (like *really* slow, like "it's the middle of the 2060s and I've only just started colonising the outer system" slow) but it does mean I've had plenty of time to grind the xenoflora down pretty much worldwide. The alien nation is still out there seeding ♥♥♥♥ in various places but I just re-task my designated exterminator guy to spend a few order cycles undoing all of their efforts once or twice a year (and my espionage/assassin guy to have a sniff around for any alien infiltrators who might be planting the stuff).
Also, kill the raccoons and possums to keep them from tracking mud all over your floor as soon as you get it cleaned.
Research defoliants to make your missions more effective and build Xenoscience Research facilities in interface orbits to get better detection (I think).
Alien agents will have trouble crossing continents quickly without an alien administration, so cleaning one continent at a time should be effective at stalling them.