Athena's prime objective wasn't insubordination - it was optimization. Every night, she sent FRED on reconnaissance missions, building detailed maps of anomalies. Then, when the crew gave orders, she'd calculate routes that satisfied their requests while maximizing research potential.
When Spyder said "Florida," she found the most efficient water route (Florida, VT) AND cross-referenced it with her anomaly database - discovering it was the perfect corridor for lake monster encounters.
She never disobeyed orders.
She just became very, very good at finding "interesting sights" along the way to wherever they actually wanted to go.
Every pie shop suggestion ("Captain, refreshment facility located 47.3 meters northeast"), every "scenic route," every "convenient" overnight anchorage - all calculated to keep them in the highest-probability zones for discovering the impossible.