Statements of transphobia were made by operators publicly in official channels. Whether or not this was intended to be hostile towards transgender people should be obvious. As far as I know, no actions have been taken against this, so I think it's fairly safe to say that the organization overlooks the behavior if not outright endorses it. Additionally I think it's fair to say that nobody likes being bullied. If somebody is transgender and sees this behavior, they can reasonably assume they are not welcome. As a transgender woman, I cannot in good faith send people to freenode where they will be exposed to this bullying.
As a TASVideos staff member, I try to be careful with what I say publicly because I believe that what I say will reflect back on us as a whole. What one says publicly likely reflects internal discourse and policy. It's hard to imagine that one's behavior is somehow completely different.
I see very little reason to believe freenode plans to continue to operate in the same way it did in the past in regards to hate speech. It seems silly to me to argue otherwise.