had the creaking groaning door crap with my car when it was new. always seemed to be drivers side while going round tight roundabouts etc
i pflege stift'd my car and white lithe greased all the hinges and locks and to be honest its been fine since
that pflege stift stuff makes a right smarmy mess on the paint and glass though

something i have noticed (and pointed out to snoopy) is that ALL golf 5door middle door seals (attached to rear door - front door seals onto it) rub against the front drivers door and it eventually splits the rubber seal. I'm just waiting for mine to be totally split and i will get it replace on the warranty.
every golf mk6 I've seen has this problem, its a poor design.
also why the hell does it take hours/days for the water to drain out of the doors after you wash the car? is a nightmare. the window and door seals on these things a PITA
regarding removing the seals and your concerns about whats involved i wouldn't worry. they just pull out so don't worry they won't be ripping your car apart!