Especially when they suggest organization wide changes to improve workflow or work environment. Don't be the guy always dismissing suggestions or you can slowly but surely turn a proactive A player to someone that just do the bare minimum while seeking other opportunities.
Also, this kind of people tends to be loyal to your product success more than you.
This will seem like they are fighting against you, but train your eyes to see the difference.
Also pair this kind of people with similar one. The goal is for them to counter and correct each other. It'll give them opportunity to grow.
I've also really enjoyed Jason Fried's talks and writings about managing employees.