Walt may have been in the clear, but he has a lot of loose ends.
His family members, who hate him and know about his involvement can testify:
Skylar - She was Walt’s “accountant” and partner in crime. She was in constant contact with Walts money and probably has some kind of evidence which would prove this. The car wash business could be investigated which could bring up some police charges.
Walter Jnr - Despite the fact that he never saw or was involved in the money laundering or any other criminal activities. He was still in the house which means he could back up Skylar’s version of events.
Marie - When Hank was investigation Walt, he showed Marie all of the evidence against him. Marie could supply the police with all the information they needed or could continue investigating herself.
Unlike all the other “loose ends” that Walter “deals” with, these are family. This is a boundary that even Walt at this stage wouldn't cross. Therefore, his only real option was to leave Alberquerque on the run.