The home side head into the clash in Zagreb joint top of the section with Belgium, while the Scots sit bottom with just two points.
Reports from the Croatia camp earlier in the week suggested they were so confident of a comfortable victory, they were debating how many goals they were going to defeat the Scots by, as they seek to bolster their goal difference.
But McGhee predicts their opponents will take Scotland seriously this weekend.
He said: "I think they're back-peddling on that a little bit.
"Looking on the internet, they're now saying they intend to give us all the respect we deserve.
"They've never beaten us. On a few occasions we have drawn with them and they know we are going to be difficult opposition, they know we've got a travelling support that will demand a performance.
"So I think whatever rhetoric was alleged to have come out, they have certainly cooled that and I think they are giving us the respect we deserve."
Gordon Greer has joined a casualty list that already included Scott Brown, James Forrest, Danny Fox, Lee Wallace, Liam Bridcutt and Gary Caldwell, meaning boss Gordon Strachan has limited resources for this match.
McGhee said: "We will pick a team and a system that we feel will give the Croats as much difficulty as we can.
"That will be selected from the squad of players we have available.
"So we are not going to suddenly try some different shape or some different way of playing or play players in a way where the balance of the team isn't right.
"We will pick a balanced team and the strongest team available on the day to do the job."
The task ahead may be a daunting one but McGhee believes the inexperienced campaigners will benefit greatly from facing top level opposition.
He added: "They can see the standards. They will see Croatia, the intensity of it.
"They will experience the fervour that will be going on over there.
"They will be around an international squad.
"Some of these young boys will be playing with boys who play in the Premier League every week.
"That is hopefully going to be a huge influence on them.
"Seeing up close the sort of players Croatia have will also be something they will benefit from.
"It's a no lose situation as far as those players are concerned."