McDonnell himself has doubled down on the furore, claiming that Corbyn shares his view on allowing IndyRef2. With a vote of no confidence looming at Westminster, a potential constitutional crisis and/or general election it's an odd time to be picking a fight with your own party, even if you are thinking ahead to forming a national coalition with the SNP. At this rate of infighting they won't even get as far as a hung Parliament in which to form a coalition.
As you were McDonnell, you're doing a fine job.