Rangers are usually given the Moffat and Chadwick stands when they travel to Ayrshire.
However, they will now be housed solely in the 4,000-capacity Chadwick Stand for the Ladbrokes Premiership clash on May 19 with Killie saying earlier in the week by way of explanation: "As we continue our 150th anniversary, we want to turn our final match of the season into a celebration of all things Killie."
A Rangers spokesman responded in a statement which read: "We are disappointed with this decision, which will force us to consider carefully what allocation we will seek for future matches at Rugby Park."
Ahead of the Ladbrokes Premiership game against Aberdeen at Rugby Park on Saturday, Clarke said: "It is not about Rangers. It is about Kilmarnock.
"It is a decision about our football club and our fans. That is the most important thing. It has nothing to do with Rangers.
"I am not surprised (by the response) but as I say, it is a decision for Kilmarnock and their fans.
"The nonsense that has followed it is typical Scotland I suppose. Typical."
With five league fixtures remaining Killie are in third place with 58 points, ahead of Aberdeen on goal difference.
Clarke believes the Dons will be smarting from their 3-0 defeat to Celtic in the William Hill Scottish Cup semi-final at Hampden Park in their last outing.
He said: "I think it will be a tough game because they will be hurting badly from last week.
"They lost the game in a bad way so they will be looking at the last five games as five cup games to try to get into Europe, so we expect a tough challenge and we will be ready for it."