Have you considered, or is it possible, to save your temporary featureclasses into the "in_memory" workspace?

ArcGIS & Modelbuilder will automatically clean up your temporary datasets once the process is complete. Also, you will likely see a dramatic improvement in processing speed with your models. Working with data in memory is tremendously faster than writing to disk.

More specifically from help: "When using the in-memory workspace, any intermediate data should be deleted as soon as possible to free up those system memory resources. The Delete tool can be used to delete data in the in-memory workspace. Individual tables or feature classes can be deleted, or the entire workspace can be deleted to clear all the workspace contents."

Perhaps you can save your temporary featureclasses into the "in_memory" workspace.

ArcGIS & Modelbuilder will automatically clean up your temporary datasets once the process is complete. Also, you will likely see a dramatic improvement in processing speed with your models. Working with data in memory is tremendously faster than writing to disk.

More specifically from help: "When using the in-memory workspace, any intermediate data should be deleted as soon as possible to free up those system memory resources. The Delete tool can be used to delete data in the in-memory workspace. Individual tables or feature classes can be deleted, or the entire workspace can be deleted to clear all the workspace contents."