My take is that McCabe presented Pence with a no win situation.

Pence was on record telling the press that there was no Russian contact, even though he KNEW that Flynn had talked wtih Kislyak.

THUS, either Pence would be exposed as a liar, or they had to go along with the FBI's version that Flynn had lied.

The choice was obvious.

Also, Flynn could go back to working his sting operation anyway.