Noone's calling it professional. Situations where the CP or Boss is deciding whether something really needs to be written up or not, and the pilots are going along with it, is a reflection on the safety culture of the company concerned and it's definitely NOT professional. It's also a reflection on the traditionally uneven supply and demand equation for GA pilots and jobs.
In companies I've worked for, I've been able to write up anything I felt required it without worrying about people getting upset over missed flights. There are some GA companies around where this isn't encouraged though.