Not an unreasonable policy in the abstract but open channels for free software projects should be publicly and permanently logged, same as mailing lists. Private channels, sure. Other than that, the project should have public logs, at which point it doesn't matter if a for-profit company wants to see those logs because literally anyone can—or could have just joined in the first place.

(Debian also has a policy that you may not publicly log its IRC channels, and I also think it's wrong.)

Sure, but I can't even reconnect with another client with my normal Freenode account now.

Hit up #freenode and see if one of the staff can mediate wih the channel ops for you - "I was banned by account because irccloud but am happy to use another client" seems like a reasonable request to me

(I'm freenode staff but currently mostly on hiatus due to lack of tuits)