The first time I threw an anti creep virus capsule, I experienced the lag that slowly returned to normal. A few hours later after all was normal I threw another one to knock down their evolution factor. There was already no creep on the map, but the lag was back. Checking time usage in mod-Krastorio2 after about an hour, there was no improvement in time spent.
To test a hunch that something was going wrong because all of the creep was already cleared, I console spawned a small patch of creep. Afterwards the lag immediately improved and started to progressively clear up as I experienced previously. It seems like the virus is getting stuck looking for creep if there is none on the map and never stops itself.