Here's my position. No idea how many will agree with it or can relate, but all I can do is give my view.
I am a full-time, unashamed, card-carrying Fed fan, and I admit that at multiple times in the past I have thought very little of Novak, essentially for the reason OP mentions (that he's been beating Federer and poses a threat to his legacy).
I admit this, and I think some of his current haters would do well to admit this too.
But right now, and as of the last nine months or so, I have come to accept it, make my peace with it, and respect Novak for the great player he is.
I won't lie and say I particularly like him, or that I am a fan of his, but I can and do respect him, and my feelings in this regard are now quite stable.
Anyway, regarding Novak climbing the ladder of history, I wish him the best.
Will he pass Federer? I don't know.
If he does, again, I'm not going to be particularly happy about it, but how can I be?
I have followed Federer for the entire time I have watched tennis, and as far as my interest in the sport goes, his victories are meaningful and joyful for me.
Of course I want him to be the best.
But, and this is important -
I can deal with it.
I can be happy for Novak when he wins, and disappointed for him when he loses - these things have happened many times in the past.
I understand that it isn't fair for me to hate on him, as he has done nothing really to deserve it. Beating Federer is his job.
I do not hate him, and do not wish him ill.
I am friendly with many of his fans - good people, and Novak himself is a good guy and does not deserve any hatred.
If Novak somehow climbs above Federer, so be it.
Even though I want Federer to be the greatest, I can deal with it if he is not.
To me personally, he always has been, is, and will always be #1, even if objectively he may not be at some point in the future.
I don't
need Federer to be the greatest, or the best. I am not a glory hunter, and those things are not why I follow him.
What Federer does - out there, on the court - is why I am a fan.