Yes I agree with you! I do believe Logan loved Jean deeply. Maybe it started as lust, but it grew to be much more. Time and again we have seen his love for Jean shine through.
Named a school after her
Came back from the dead to save her
Killed her as she could not bear dying an agonizing death by the sun
Killed her again in Endsong while admitting it hurt him a lot to do so
Wolverine goes to hell, he came back only because of Jean's memory he harbored.
He even had a special room in his mind dedicated to just Jean
Lastly, when he died, he thought of Jean.