Hm. In a wide-open area, Group Fly shouldn't have affected teammates too much, as long as OP was fighting mobs apart from everyone else. But during, for example, the computer fight (with or without Rommy and Requiem), GF would have been disruptive. I don't remember what the radius is for GF, but if you can't be far enough away for it to not affect the rest of the team, especially during a boss fight, and you're asked to turn it off, better to do so.
GF is certainly useful versus the Hami Seed, and during the Mito portion of a Hami Raid, and during the pylons and bomb placements of an MSR, but would be unnecessary for the Hami end fight or in the bowl.
Before this thread, I didn't realize that one could not interact with Null during a TF. Maybe that's to prevent people from switching alignments mid-TF? (If someone switched to Villain during a TF, or to Hero during an SF, would they be auto-booted or would that crash the whole TF/SF?) Just wondering if it would be easier to allow Null contact during TFs than adding "Disable Group Fly" to Options, which has already been established as being difficult/time-consuming. Not that the devs don't have enough on their plates already.
I guess the bottom line is uphold Wheaton's Law, be prepared to compromise when you're on a team/league, and if you can't do that, soloing is always an option.