I don't think it's a bad thing. Like them or not, they have a somewhat controversial history; a lot of people worried that their projects would fork the ecosystem, or give them too much control of it - I wouldn't be surprised if they decided that it would be better for the foundation's goal of being a community effort to not be seen as having a heavy hand in it. Some people have expressed similar concerns about Facebook and IOHK as well, just from the financial influence they might have, even though their haskell projects haven't been as close to critical infrastructure as FPComplete's have.
FPC is not that crazy of an organization. Yes, I know in the past there's been drama between its members and other haskellers over stack/cabal etc., but I'd feel more comfortable if the Foundation were able to muster the diplomatic finesse to overcome that.
They are not crazy, they are just of the "I'm doing it!" instead of the "Do you think this is the best?" kind of people. They created some very good stuff (yeah, stack is great, even though I mostly stop at cabal myself), but that's not a committee member attitude.
Anyway, its not a big deal. I even doubt they will have more or less influence over anything because of that decision. It's not like unofficial communication will stop.