The Germany and Real defender risks a 12-match ban after throwing an ice-pack in the direction of match officials at the end of the Copa del Rey final on Saturday night.
Rudiger lobbed the ice-pack from the bench as Real were losing to Barcelona and was shown a red card after being substituted.
Kroos said on an Icon broadcast: "I totally agree with Felix (Toni's brother) when he says that people are now calling for his exclusion from the national team... especially people who, at the time, would have deserved to be banned themselves.
"I wrote to him after the match, and he himself is aware that it was probably a series of linked errors that night.
"We must be aware that many do not know what really happened. It was a Clásico, a cup final, he fought like a lion, he has had knee problems for weeks, there are various incidents. But now he will receive a sanction, and that's it.
"We must not pretend that he killed someone. We must always be careful not to automatically follow the flow of collective indignation."
"He was out of control"
Meanwhile, Germany World Cup winning captain Lothar Matthaus offered much stronger criticism of Rudiger's actions.
He stated: "He seemed to have gone mad, he was out of control.
"He's a German international, he should be a role model but he's completely forgotten about that. If he gets away with a four-week ban, he'll be happy. I'm thinking more of a double-digit ban. I expect a massive ban."