A plaque created by Joshua's grandfather and erected on Reignier Catholic School wall had previously been suggested as an alternative outcome, but this is unlikely to happen.
Joshua's mother, Tracey Gibb, felt the decorations served as a safety reminder to children as well as a place Joshua's young peers could acknowledge him.
Reignier principal Julia Johnson said yesterday she and Ms Gibb had previously discussed erecting the plaque on the school wall.
Although she was receptive to the idea, they decided the school wall was too low and it would be ineffective.
"We had a conversation about it. Unfortunately we both came to the decision that the actual fence itself - we've got a very low brick wall - and there wouldn't be anywhere on it appropriate to put it. As much as we were open to it, it probably wasn't the best place to put it."
The story provoked a strong reaction on Facebook yesterday.
Emma Hargreaves wrote: "So sad that the flowers are to be removed, I feel sorry for the person who complained as they obviously have no heart."