Lyon had an out-clause in his contract with St Kilda, so the Saints should have known Lyon had the right to leave. In that case St Kilda had the choice to either lock down the coach or move on. They hesitated – which is understandable given the position they were in – and Lyon took the long-term offer in front of him. It’s probably not how I would have handled things if I was Lyon or Fremantle, but I also thought the moral panic it set off in the likes of Gerard Whately was overwrought.
I’m assuming Freo didn’t offer Lyon an out-clause, meaning he is still under contract for next year. That gives Freo a bit of leverage. Personally, I’d hope Freo’s admin and Lyon had a good enough relationship to have an honest conversation about where they each see themselves in the coming years. If they don’t have that relationship, I think a mature way to handle it would be to tell Lyon that he wouldn’t be receiving an extension this year, but that if he wanted to talk to Carlton about their position he could do so with the club’s blessing. You might even go as far as to amend the contract so that there was a reciprocal out-clause at the end of the year.