When driving to UK a couple of weeks ago they took away my wife's ILR citing grounds of being away for more than 2 years. Never a problem before. And gave us a six months visa for being honest

We don't intend to leave CH but what is the best course of action please to either get it back or have a hassle free alternative to the UK for free movement back and forth?
They said at the border that the best alternative is an EEA Family visa. Is that true?
Thank you.