Honestly, their video - and more specifically the way they've presented it - makes me only more certain that they're not mad that Ned was coming around, they're mad that the negative public perception has forced them to act upon it.
They have proper thrown him to the wolves, and there really wasn't any need. They could've said Ned is taking time off to refocus on his personal life, and before his return, will undertake a mandatory HR programme on appropriate behaviour in the workplace. I think I would have respected that more than the "he's not our problem any more, please don't stop watching" approach they have gone for. Especially when Zach took that moment to explain how they'd lose so much money from videos they can't release now...
Also, interesting confirmation that the Ned and Alex affair was a) long-standing, and b) "romantic" in nature. Sounds like Alex has privately confirmed to them that it wasn't coerced or anything.