To remove the mandatory Department/Class/Location while creating the journal entries.

1. Navigate to Setup > Accounting > Accounting Preferences > General tab
2. Allow Empty Classifications on Journals: Select True

 This would allow Journal Entries to override any other preferences set for mandatory Classes, Departments, and Locations, and then the user can create a Journal Entry that 

has line-items without Classes, Departments, and Locations, even if the user requires them on other Forms.