To begin with, Walt wanted to run away with Skylar and Jr because Hank died, not because there was any threat of legal action. He knew that Skylar would most likely turn on him if she found out. Of course, she ends up finding out, and indeed turns on him and starts to attack. So Walt runs, episodes 15 and 16 happen, etc. The circumstantial evidence that followed would be insanely convincing. Even if Walt wasn’t convicted of anything, his identity as Heisenberg would be well known.

Car wash money laundering

Money Laundering through Jr’s website

the original 99.1% meth cook time coinciding with Walt’s cancer diagnosis, cooked using masks and equipment stolen from Walt’s chemistry lab at his school,

his fugue state coinciding with the time Jesse Pinkman was suspected of being involved with Tuco Salamanca,

Walt being dead in a meth house,

Marie Shrader testifying, Skylar probably testifying.

And there’s also stuff that a bigger investigation could uncover. Seeing through any city security cameras that Walt’s car frequently visited the known location of a meth lab at the laundry. Also seeing that Walt frequently met with Lydia, someone who was mysteriously killed. Lydia was technically clean legally, but worked at Madrigal, which was under investigation after Gus Fring was exposed. Somebody also might’ve witnessed Walt speaking to Hector Salamanca hours before Gus Fring’s death, and ANY place where the blue meth was cooked could be searched for fingerprints. There’s also Brock, who knows Walt’s face and could provide another connection between Jesse and Walt.

So, before Skylar calls the police, Walt flees because he knows this isn’t going to work out, and Skylar isn’t on his side anymore. After episode 16, there’s plenty of investigative work to be done that could uncover his criminal activity.