I think you're conflating two different issues here aren't you?
You're correct that Sky can't restrict channels from being in the EPG if they are FTA (or pay Sky to be FTV) - if they pay Sky to be in the EPG, they are in the EPG (subject to slots being available)
However that doesn't mean Pay TV channels can demand to be part of a Sky subscription package. Sky can absolutely decide that they no longer want to pay third party channel operators for their channels included in Sky TV pay-TV packages. Sky are well within their rights to decide that the value added by a third party channel or channels being present in a pay-TV line-up isn't worth the money they are paying the channel operator, and can drop them.
If that channel operator wants to go FTA and be funded by advertising, or be funded via a separate bolt-on subscription (which they'd pay Sky an amount to manage) they could do that - but third party channels don't have an automatic right to be included in Sky's pay-TV line-ups.
Remember when Eurosport were dropped by Sky briefly after they failed to agree terms. This is not really different to that.
Stuart and London Lite gave kudos