I agree with what you've done. I personally prefer having the leg room in front of me, so I usually put my backpack up top after I empty out the things I'll need for the flight (tablet, headphones, meds, etc.) so I don't need to go back into it. I'm not going to make myself more uncomfortable for a flight because someone bought a cheaper ticket and did not get on as early as me. As far as I see it, that's a perk of being an Elite or purchasing a non basic-economy ticket.

And if the airline has an issue with it, from my prospective, they are the ones who caused these types of issues by charging so much for checking luggage and cramming the seats so close together.