Well, I'm going to be honest here:
The lantern should and does have counterplay. Now, I use it like a dirty bastard because I don't like Thresh, but if RIot deemed sitting on the lantern to deny it is unfair, then it's unfair in the same manner it would be to somehow have the ability to cut Tahm's tongue so he can't eat an ally or something like that.
The real counterplay to the lantern is zoning someone away from it in the first place. A Nautilus, for example, can properly block the lantern to delay an enemy long enough to die before they can escape. That's fine. A Sona without her ultimate should not have the same capability just by standing there, if Riot has deemed that unfair.
Now, zhonyas and flash do have some measure of counterplay, and I think this is where I'm getting at as well. It's all about the set-up. Someone in zhonyas can't do anything, so you can set something up like a Teemo shroom to catch them afterwards. If you know someone is going to flash, you can lead the opponent with a skillshot or flank them. Which is fair. Taking away zhonyas and flash, however, would feel like utter bullshit and I think that's where you're getting at.
So I guess while I may do it (because I don't like Thresh), you make a fair point and there are already ways to counter the lantern that are fair enough as is.