Is pop up always bad?

I am involved in a redesign project (web app) where existing system throws quite frequent, random pop ups. These pop ups are used to gather information and also to display information and confirmation. Considering just to enter 1-2 form fields or checking and applying filter criteria popups were used. I am trying to get rid of these redundant pop ups. Now stakeholders are insisting on keeping most of the popups as they think users are very well acquainted to the system.

I am facing hard time convincing stakeholder 'why pop ups should not be used or atleast minimized' Any guideline/research suggesting scenarios for proper pop usage (when to use and when not to) will help me understand and convince stakeholders accordingly.