Not sure about the details with Freifunk, but Guifi has collaborating companies who basically operate like ISPs but connect you to Guifi + you get a internet connection via the Guifi peering the installer helps you with.
The idea that anyone is too firmly entrenched is always true. Until it is not. We are not still using horses, nor casting bronze tools. Nor do most ships sail. We (mostly) don't burn coal anymore. It would have been utterly insane to imagine replacing any of those entrenched technologies. That is the "follower" syndrome.
The context for a new kind of internet is very different now, than when the internet started. That changed context provides an opening for new ways to do things.
A crucial and hard piece is that it has to be paid for. As much as you need a parallel networking stack you need a parallel business model. Yes, the current one is too firmly entrenched, etc.