Although I like your idea, I'm pretty sure that there isn't going to be any cost for changing schemes for the coach other than the OVR of some of your players temporarily going down and your scheme fit percentage going down as well. Your players won't get bonus XP to speed up their progression if they don't fit your scheme though, so there is that as well.
The article talks about changing your scheme and getting different players to build around a QB that unexpectedly fell to you in the draft, so it seems like they designed it to allow the User to change schemes at will with the only consequences being the ones list above.