Converting a large number of blocks produces an incredible amount of particle effects, most noticeable when the flower is first placed in range of the target blocks.

Cranking down the particles in the video options helps significantly, hopefully they'll be further improvement by disabling them outright for a particular flower.

Specifically I've made a flower (Shimmering Daisy) to clear out Thaumcraft taint (on the surface only), there is a massive lag spike when the flower is first placed as it initially targets all the taint- after which the performance is fairly good as it keeps the area clear.
Placing the flower in a taint free area produces no noticeable performance impact.

The flower
https://github.com/CelestialPhoenix/BS-G-1.12-Pack/blob/master/config/morechids.json

The recipes for clearing taint.
https://github.com/CelestialPhoenix/BS-G-1.12-Pack/blob/master/scripts/All%20Recipes/BS%26G%20Morechids%20Shimmering%20Daisy.zs