Totally thought it through!!
For me I don't think a challenge system would work, as I could see teams using it on occasion just to take the pace out of the game if they were on the back foot. Challenging for the sake of challenging.
I think a video ref would be better. Someone scrutinising the game for anything the ref may have missed. Relays a message to the ref and action can then be taken on the field. The main downside of course is that the retribution wouldn't be instant and would be maybe 20 seconds to a minute later, but play would continue. after all, these are things the officials have missed anyway.
This then wouldn't disrupt the game to any great degree and like tonight, we could see justice done during the game. Same last night with Suarez, though that one needed very close inspection and freeze frame of course, so may not have been spotted.
Tonight was clear cut.