I doubt they thought that way. The dev team put Blue in the Tower because it is a required stop in the game. It is the same reason for the awkwardly placed Sliph battle. The player has to enter the Tower to complete the game. They dumped Raticate because Champion Blue cannot be carrying such a normal Pokémon. And he realizes that Raticate isn't keeping up hence being the lowest level at the Anne battle.The full logic is that the Raticate disappears when you battle Blue at the Pokemon Tower. He has a rat for a few battles, and then you fight him in a graveyard and he doesn't have a rat. Considering this is the only time Blue drops anything from his team, and that the game gives no explanation or even acknowledgement of the rat's absence... I dunno, even if it wasn't intended, I'm sure someone on the dev team realized "hey, this kinda makes it look like the rat kicked the bucket".
Pokemon Tower is also the battle where Blue rounds out his FWG core with two of Growlithe, Gyarados, and Exeggcute, which leaves an empty slot open that won't be filled with Rhyhorn until the battle on Route 22, near the end of the game. Surely if they wanted to do some environmental storytelling that implies Blue has just decided to stop training his Raticate, they could have done something like leave it on his team but keep it at level 16.
No one thinks Hop's team keeps dying, much less being killed by Hop himself. Unlike Blue, the game explicitly gives a reason for why Hop keeps changing up his team, and never places Hop in a creepy graveyard to give implications where the game refuses to give explanations.
EDIT: Also, whoever said anything about Blue killing the rat?
Well, Blue seemingly only uses in battle what he considers (at the time) to be relevant. He mentions catching Cubone in the Tower and on the Saint Anne he mentions having catching 40 kinds of Pokemon yet he doesn't use a full squad until after the 8th Badge.
Serena in XY starts with a Fletchling and catches a Bunnelby but both are quickly discarded despite the open slots on her team.
The same thing the PC first does when he arrives in Lavender Town: checking out a local landmark which contains catchable Pokemon. And Blue even mentions catching a Cubone there.I guess the whole matter is the "Your Pokémon don't look dead!" phrase Blue says. Sure, he says that in a "Why would you be here in the first place?" kind of way, but... what is Blue doing in the Tower? He doesn't have the Silph Scope so he cannot train there... (apart from the Channelers, that is)
Not only does he drop the rat, he also dumps his Fearow.I do find it interesting that they kept that Rattata swap in place in the sequels. Not just FRLG, but even in Yellow, where his team is completely different, Blue gets rid of his rat at exactly the same point. I agree it was probably coincidence, because the writers at the time didn't do subtlety, but it's odd thing to keep between games.
Giovanni dumps his Onix after the Game Corner and his Kangaskhan when you face him at the Viridian Gym. Now while you can argue that he is using his Gym Team (even though it can said that Gym Teams are the Gym Leader's personal Pokemon), it is not like Onix and Kangaskhan are that different from what he uses at the Gym. He uses a Rhyhorn at the Game Corner and Sliph. Onix is part Ground type. And Kangaskhan feels close enough to King/Queen in traits. But no one is out there saying the PC killed Fearow, Onix, or Kangaskhan.
That does raise an interesting point about Giovanni though. If you say the Pokemon he uses in the Gym battle aren't his then the man carries around some weak Pokemon (for a crime boss) while carrying three Pokemon that he uses in the Gym Battle (not helping his cover) suggesting the Gym Pokemon are his personal ones. Also corroborated by the fact that when Blue is Gym Leader he uses his own crew. He is darn lucky that Lance or another Elite 4 member didn't show up.
Of course, his team has to be weak so the PC can advance in the story. The anime and the magma correct this by giving him a diverse roster. (Frankly, Giovanni seemed too pragmatic to be shackled by devotion to type) Origins also handles it well by having Red lose during their first encounter. Ah, the nuances of gameplay/story.