I haven't battled very much since the major gym changes (truthfully, I've quit playing mostly because of those changes) But anyway, today I beat a raid boss before the gym raid began. It said "You Won" and gave me rare candies & let me capture the Bayleef that was the holder of gym. Now there is an icon that shows as controlling gym that is orange/gold shield with the head of a Rhydon in it. I can't put any of my Pokémon in the gym. What does that shield mean?
As mentioned above, this is just the victory icon that appears after you've defeated a raid boss. That icon won't disappear until the raid boss leaves.
While a raid boss occupies a gym (regardless of whether or not you've defeated it), the Pokémon defending the gym are not able to be battled. Due to this, it's not possible to remove opposing teams' Pokémon or put in your own until the raid boss is gone.
Once you have defeated the Boss, you won’t be able to interact with the Gym until the raid has completed. After the Raid Battle has completed, the Gym is restored to its state before the raid.