If you read the article, you’d see this from the CNO:
“The determination that I just mentioned about his not being reinstated to command, and the action holding the strike group commander's promotion in advance, that's not about the email that he sent, and it's certainly not about the fact that it leaked," he said.
"Captain Crozier hit send once in that email. Captain Crozier did not leak that email or intend for it to be leaked. So at that time, I felt that the facts did not justify relief based on the narrow scope," Gilday added.”
So maybe he was initially relieved for the email and leak, but both investigations found this was not sufficient for his initial relief or the upholding of his relief. It seems this is the reason for upholding his relief:
“The results of the latest Navy probe faulted Capt. Brett Crozier for several missteps, including not adhering to proper protocols to prevent the pandemic's spread on the ship, such as social distancing, and being too slow in evacuating sailors from the ship once it arrived in port in Guam, they said.”
Now, having been on navy ships before, I have no idea how anyone could seriously think “social distancing” would be possible (bunks are stacked on top of one another, crew’s mess is shoulder to shoulder, passageways require you to turn sideways to pass somebody, etc). the evacuation piece is interesting as I thought that’s what CAPT Crozier was advocating for in his letter, but I’ll assume the later investigation found something about this that’s not being elaborated on here.
I’ll not comment more on the CAPT’s removal, but I will say any CO that says the ship is more important than the sailors doesn’t deserve to be in command. After all, a warship without a well trained crew may as well be a target barge.