There is a spell in Khrysalis that takes Rank 1-7 pests for 48 hours away and I think it is called crop watcher, but it needs level 15 gardening, another thing is a the gardener in Av, I think he gives a pest bomb spell that destroys up to rank 6, not sure though. Hope this helped.
I'm having the same problem, I got a Queen Crape Myrtle seed dropped in Khrysalis, planted it now I can't kill the pests. I wonder why KI would allow me to plant a seed that I'm not high enough gardening level to kill the pests it may get? Weird. Idk whether to dig it up or let it die and revive it when I reach level 15. Wiki says you need Ant Lion to kill it but there's no info as to where to get Ant Lion. Lol!
You can use the Summon Pixie spell. It's expensive - 150,000 gold - and very hard to cast - 25 energy per plot (!). But that's what i'm doing until I can get the other pest spell. The other thing you can do: Once you get rid of all pests and needs, don't ever visit your plants (unequip your house if you have to). They will continue to grow all the way until Elder with no further problems - you just miss out on all the harvests inbetween :( The only other option I can think of is: let them die and revive them later when you have the pest spell.