Only by killing him, will you keep what made him amazing intact, will your viewers not only not hate the show for screwing the villain up, but appreciate you for keeping the villain's integrity intact, and will happily follow you on the rest of your journey.
No, the viewers will hate the writers for killing off the only good villain the show has ever had and replacing him with villains who aren't nearly as good (because killing Sylar means you lose Quinto, who was the only reason we liked Sylar in the first place). Robert Knepper being such a dud as Samuel proves that even if you hire an excellent actor to play the next villain, that doesn't guarantee that shitty writing won't sabotage him beyond the ability of any actor to repair.
Bullshit. We liked Sylar before Quinto even played him. And you're contradicting yourself. If the writing is so important, than Quinto is unimportant. Any actor in a well-written role would have produced the same effect, and here's the rub. The reason why everything went to shit has got nothing to do with any actors or characters, it's the writing. Good writing will have a great show with people coming back to watch it. Keeping a villain around and trying to make him work as not a villain, but not quite, a villain after all, is BAD WRITING. Result, a bad show, and you lose viewers, fast. There are a lot more viewers that left, then there are those that stayed because they liked Quinto, and are willing to watch despite the bad writing.
Thus, if the show had continued to be well written, instead of trying to pander to what they thought was popular, Sylar would have died in the S1 finale at the hands of Hiro, Peter would have blown up and be vaporized and dead, and the remaining heroes would have formed the Avengers.
S2 would be them staying in touch as the right wrongs, until they come across something they have to face together, they get together again and face the threat together. That would have been a show worth watching, that would have been good writing.
If the writers had done the "right" thing and killed Sylar before anyone started to hate him, it would be the "stupidest thing they ever did" and "the reason the show sucks now."
Nope, not at all. Maybe a tiny minority Quinto fans would say that, but the large majority would be enjoying the good stories. Pandering to what and who you think is popular, as opposed to writing good stories, will lose you viewers. Continuing to write good stories, which would have meant Sylar dies, that would have kept your viewers, and they'd still be praising your good writing today.
The solution is not to fire perfectly decent actors. It's to hire the writers who can't figure out how to make Sylar work as a character long-term. Sure, it's a tough assignment, but wouldn't you expect the writers of a high profile network show to be the best in the business? If they want to prove what hotshots they are, here's their chance.
Sylar cannot work long-term. Making a psychopath work long-term, can't be done, because the only way to do that, is to remove the psychopathic part of them, the very thing that made him popular! You can assemble the greatest writers in history, and they can't do it, because it can't be done by definition. You immediately destroy what's popular about him, and thus the character fails, and CAN NOT work. For a villain to have a shot at remaining a good character, he can only stay a villain. At that point, you have three possibilities: either lose his menace and thus not remain a good character, be Lex Luthor; some CEO beyond the touch of your heroes, protected by law, or get killed off. A individual psychopath like Sylar can't be / become Lex Luthor because it destroys the character, that leaves only get diluted, or get killed off.
Good writing means, he gets killed off.