Is rhydon a good counter against muk?

Yes, Rhydon quad resists Poison and Muk is weak to ground.

With the update all defenders and all things defense took a major hit. So his weaknesses aren't really much worse than those around him

Just don't place a Muk after something that is also weak to ground so that the attacker has to switch to exploit the weakness/resistance and can't carry over energy between fights.

Muk was always good, GamePress just underestimated him in their earlier lists.

Neither gym attacker/defender lists or raid counter lists are perfect, and players should keep that in mind. On every single list a few mons have either been left out or slightly misplaced. The lists should be seen as a set of guidelines, not as a complete compendium on viable pokémon.

That aside, you're right on the Rhydon matchup. It's a bad one for Muk.