The best way to counter Assimilate is to not play Tech 1/2 Upgrades/Buildings that your opponent can use (Ongoing spell rarely fall into this category, but I have used it against an opponents Mind Control on my Immortal).
Every colour has powerful options that you have to play around, it is the same way you wouldn’t play a single large blocker against black, as Sac the weak or Hooded Executioner can ruin your day. Or pump a lot of gold and cards into a Hero against white due to Snapback.
Now given Assimilate is a spell, you can also do the normal anti spell options, IE kill the hero that casts it. That a) makes me have to put another 2 gold to take your garrisons (which just becomes levels for you, and reduces the amount I can make use of the garrison when I take it), and b) gives you a safe turn when you know it can’t be taken (and if my draws are bad, that can easily extend to 2/3 turns…)
TBH I don’t think Assimilate is stronger than Nature Reclaims. In most cases it is weaker, as it clogs up your deck if they can’t remove their own upgrade/building, and if they can, then you have to keep playing/cycling correctly to have it at the right times, and costs more gold. In the small cases when you can also make use of the upgrade/building (as was the case here, when I chose to not do my normal Tech 2 Present rush, so that I could make use of an assimilated garrison), then it is stronger, but most of the time, your opponent doesn’t play the upgrade/spell, so you’ve committed a resource to counter nothing…
An Art of War build is where you focus on Oni’s ultimate spell. Given a 6/7 Swift striking, Unblockable, Frenzy, Readiness hero can easily destroy your opponents tech/base, and defend easily, it can be very hard for a codex with no hero removal to deal with. A good example would be my last game in the King of the Hill series. I chose a strat that couldn’t answer it, and was forced to watch my base get destroyed.