I am not sure that Merdaneth was complaing about popularity being unfair. I think his point was only that players tend to be a lot more forgetful and easy with characters belonging to players they like OOC.
OOC popularity is simply something you'll have to consider when you plan your character's career.
If you piss off a CEO in OOC chat, and then proceed to apply for said corp a month later, be prepared to be rejected even though characters with a much more checkered past than your own are accepted. OOC trumps IC.
If you switch from Amarr loyalists, to pirate, to Republic loyalist, to Sansha loyalist, to Blood loyalist and then apply for your original Amarr loyalist corp again, and you were/are well liked by the members, then you'll get a token 'repentance' assignment and are quickly accepted back into the ranks again. OOC trumps IC.
IC considerations are important of course, but IC defections, betrayals and similar stuff are easily forgiven, while OOC defections and betrayals are not.
If you make few OOC friends, and many OOC enemies, better be prepared that any sudden changes in your IC playstyle will not be forgiven easily and any attempts at retcons will be hindered by people coming out of the woodwork pointing them out. Your character may suddenly feel 'locked' into a certain playstyle if you lack sufficient OOC support.
My only issue tends to be that many players justify such things by saying 'hey, I'm just playing my character'. In my opinion, just because the reasoning is IC, doesn't mean the motivation is.