Don't people fly separately and meet up at the destination??
We do that all the time, not for frequent flyer reasons but for all sorts of other practical reasons (having said that, we have even flown in separate cabins on the same aircraft due to his company policy, which I have nothing to do with) and I don't see differences in alliance or airline would be any different.
If my husband was a die-hard Ryanair or SkyTeam fan, I'd let him get on with that, and meet him at the destination - I'd fly either a Star or OW carrier and meet up there.
Someone asked him if we didn't want to be flying together, and his answer is "All she does on a plane is to sleep. She's not much use as an in-flight entertainment". That is entirely true, and I have no objection whatsoever.