Let me make it clear there is distinct tongue in cheek element to my original post and it was probably just done to add some lame comedy to a lame film....But at the same time I can't completely dismiss the possibility completely that Shatner made some conscious effort on some level to degrade the Enterprise's role so as not dimish his role.
Look at it. it TMP the ship is given massive screen time and is strong and heroic in that it stands to up an attack from V'ger and helps solve the mystery. In TWOK it goes toe to toe with the Reliant, usually being the more damaged ship, yet ends up victorious at the end and heroically soars away just before Genesis explodes (Even though it was Spock's actions that made that possible). In III it puts one over on all of starfleet, even making the shiny new Excelsior look foolish, transports the guys to save Spock and even gets the drop on a BOP before it all fails yet it still serves one last noble purpose in taking out 6 Klingons and making it easier to save Spock in it's last act. In TVH it plays no real role. In TUC it's the ship chosen for this historic peace opportunity and manages to, with Excelsior, save the Khithomer conference from being destroyed.
So in those 4 films the Enterprise had a major role that featured it as a strong and valiant ship. Yet in TFF, the ONE film that just happened to be directed by Shatner, it's reduced to comic relief and is basically just a transport that has no moment of glory.
I don't know William Shatner or his mind. But there has been enough evidence in the past to show he can't stand anything that detracts from his magnificance on screen. He made every member of the Enterprise crew except himself look weak to some degree in TFF.....Would he feel threatened by a character that isn't even alive if it had a heroic moment that detracted from his awesomeness? I don't know, but I can't say it isn't possible and since he got to call the shots on this film....it seems a little fishy to me.