Omniscient Reader's Viewpoint by Sing-Shong isn't quite an isekai and doesn't quite have it 'all as a lie', but does play with some similar themes to the Truman Show of everything the characters doing being watched by an 'audience,' and scenarios being staged for the entertainment of said audience. It also raises a lot of questions about the line between a 'person' and a 'character', whether 'fiction is becoming reality' or 'reality became fiction'.
The Warrior Returns by Narack and Fungback could also be what you're looking for. It has one character who's quite crafty, not quite aligned with the heroes or villains but rather assisting both as it suits his motives, who creates what initially appears to be the main conflict for as-yet unknown reasons, betraying people who considered him allies, screwing said allies over, and creating events that lead to millions of people getting killed.
And yet, all this seems in service of destroying a yet greater evil... if his internal monologue is to be believed. The extremely vengeance-driven protagonist is now being forced to ally with multiple former-allies and cowards, including this guy, and everyone he once truly trusted is dead.
My own story also involves the protagonist having the rug pulled out from him in a pretty major way about something he took for granted, though it's not really an isekai, and maybe not as extreme as you were hoping for. (And we're a ways off from that revelation anyways.)
...That said. That doesn't stop me from wanting to make an isekai even more like what you proposed someday. If the protagonist is completely new to the world, then that should make it incredibly easy to mislead them and lie to them about who the 'good' and 'bad' guys are, right? Yet every time I see an isekai going in that direction, the protagonist is immediately deemed 'useless' and discarded, or otherwise somehow split off from the main party, so actually it's not that they're being misled but really they're the only one who knows The Dark Truth, which is... fine. But I've seen it a lot now and am pretty unimpressed by all but one story that uses it.