When you stop and think about it, by the time the movie was being made (2004-2007), Oakley and Weinstein hadn't been involved with the show in years. Their last season was S9 (1997-1998), which overlapped with season 8 in post-production, therefore they helped Scully during that first year of his (as EP).
Then they created the ill-fated Mission Hill (1999-2000), spent a year on Futurama (2000-2001), and then moved on to other projects.
Meanwhile, former showrunners like Mike Reiss and David Mirkin have kept themselves involved with the show as consultants for pretty much forever. And Mike Scully produced the film with Al Jean, as well as remaining a part-time consultant ever since he showran his last episode. In fact, if you look at who wrote the movie, it was pretty much people who were either still involved with the show or had just recently left (Meyer left in 2004, Swartzwelder in 2002, Vitti in 2003). Reportedly, Swartzwelder campaigned to be a part of the movie's development. Reiss and Vitti were already experienced in animated feature films with the first Ice Age.