#1 Pronger wouldn't be able to suspend anyone...that is not his role...Quintal makes those decisions...all Pronger and other members of the department would be doing is reviewing incidents and offering opinions.
#2 Pronger would clearly have no input on anything to do with the Flyers.
The problem with #2 is that there could be many games that indirectly impact the Flyers, especially as the season wears on.
Say there's a game late in the season and the Pens are playing Edmonton. Malkin throws a cheapshot and it actually gets reviewed and he could be suspended. The Flyers are in no way involved, but if it's a tight playoff race and the Penguins losing Malkin for a number of games could impact the Flyers playoff positioning.
I don't know that Pronger would actually let that influence his decision, but he is being paid millions of dollars by the Flyers. They've taken good care of him since his injury. Even if it's not conscious, there's probably deep loyalty there.