Would you like to name a few examples of the game discouraging thok usage, because I can't think of any place or moment where the game was actively telling you not to thok here
It's going to differ based on player skill. We veterans aren't going to encounter this as much because we are good with the thok. For unskilled players however, these moments are all over the place. The first noteworthy one is the elevator shaft in Techno Hill that I've been bringing up. You must navigate through this elevator shaft to get into the room that houses the button you need to press to turn on the power, unlocking access to the elevator to progress through the stage. this is the first time that trying to recklessly thok your way through without really knowing what you're doing is likely to get you killed, as falling in this section can be quite deadly and you're not particularly likely to land on the elevator in the middle of the shaft using the speed that the thok gives you.
There are also many other less severely punishing moments in Techno Hill that don't necessarily kill the player for thokking and thus overdoing their jumps, but they do hurt or inconvenience the player for doing so by having them go flying into an electric floor or into the purple goop. While not as actively killing the player, these moments can start to reinforce the mentality within a new players mind that using the thok is a bit inconvenient at best.
Castle Eggman is the first time we start to see platforming sections that look like little islands of traversable terrain suspended above chasms of death pit, littered with obstacles for you to carefully dodge around to get across. Thokking at a bad moment during a jump can send you flying off the edge and down to your death, something unlikely to happen to someone who knows what they are doing but likely to happen to players who are still learning the ropes. For new players, Castle Eggman is where things really start to slow down to a crawl as you start having to much more carefully avoid the hazards in your path. The thok is a bit unwieldy for new players here, as while skilled players see it as a way to clear larger gaps and as a safety net, new players see it as a cannon that could shoot them off the edge or into a swinging mace ball at any moment.
Also introduced in Castle Eggman are the enemies with shields. Thokking into these shields can send the player flying in a seemingly random direction based on how they collide, which can send a player who is too reckless falling to their death.
Arid Canyon is largely more of the same, especially in regards to the ropes suspended over bottomless pits that you must patiently wait to cross. Skilled players can thok their way from rope to rope to clear these sections rapidly, but new players are likely to miss and get sent cascading down to their death below. The boss, Fang, also actively punishes new players for using the thok during the second phase of his fight by sending them flying off the train and to their death after collision with him. Or, the player can just be too reckless and thok off the train by accident without touching Fang at all.
By the time you get to Red Volcano as a new player, you've likely already learned that thok is a very risky move to use, because it's probably the biggest contributing factor to the low lives counter you are likely to have by this point. Now in addition to bottomless pits, you have lava that hurts to touch, eats your rings on contact, and kills you when you have none. This is paired with the Pterabytes, which will pick up reckless players and drop them into the lava. For a new player, slow and steady wins the race here and you're very likely to spend upwards of 15-20 minutes in the level just carefully avoiding everything hazardous while a more skilled player can fly through the level and clear it in ~4 minutes.
Egg Rock is by far the most harsh with its use of careful platforming that can be punishing to reckless new players who don't know how to use the thok properly, and this is especially an issue since the lesson new players have been taught by now is that using it makes things harder, gets them killed, and isn't needed to progress. Yet again, the new players progression through the zone which is likely to include a few game overs is going to be more carefully avoiding anything dangerous while trying not to thok into a pit or lasers or etc. The race against Metal Sonic rewards skillful play with the thok, but can easily punish unskilled play the same way as any other level and this is with the added pressure of being under a time limit. Then you get to the fight against him and thokking into him after making him vulnerable is likely to rocket you off the elevator at high speeds to your doom or into the electric fence if you're not careful about your aim.
Brak Eggman does the same thing, unskilled players thokking into him while he's vulnerable will likely go rocketing off the edge of the arena to their doom.
This isn't even every single moment in detail, and I've already described a significant chunk of the game. While for most games this would basically boil down to "Git gud", the problem here is that new players aren't given any reason to at all. The lesson they are actively being taught by the game is that they don't need to get good with the thok because they can succeed without it and using it is likely to get them killed. Their final impressions after beating the main campaign at this point is often that they don't like the thok because of how hazardous it was to them in their playthrough. This is all too often the case with people playing through the game for the first time and streaming it and/or making a review about it. New players don't like the thok because it's bad for their health and they don't really need it.
This, ultimately, is the reason why STJR has gotten the impression that the thok is bad and needs to be replaced. They're listening to the opinions of these people playing the game for the first time and coming to the conclusion that the thok is problematic. And in all fairness, the criticism itself is fair, the problem is that too many people are misunderstanding the problem surrounding the thok, blaming the thok itself when it's the situations new players are being thrust into with it that are the real issue.
The player should be thrust into level design early on that teaches them the merits and usefulness of the thok so that later into the game they can make skillful use of it that doesn't screw them over. Many of the examples I've given in this reply would be much less problematic if new players had been taught by the game to use thok properly leading up to these moments than they actually are in reality.