And then, of course, you wait and see if the predictions of the models come true. You can't reset the world and re-test it, but you can re-run the models and ask for more prediction in the future and wait some more.
Climate scientists do both of those things all the time because they're in one of the most heavily scrutinized fields.
Isolating variables just means you compare two setups with everything the same except one. That's actually one of the things the models are for. You can't re-run the world without humans, but you can re-run the model with humans turned off.
Then someone else can do the same with their totally different model. And if both of your answers match reality with humans on and each other with humans off, well maybe the difference between humans on and humans off is the impact of humans. Or maybe not. But adding more different models helps.
In short: climate science generates testable hypotheses, does replication, and isolates variables. It's possible they're wrong (and publishing source code is a good idea) but they don't have a methodology problem. And they're probably right.
Also, Michael Crichton basically wrote Hollywood scripts in novel form. He's not a good source on anything.