Have McLaren ever denied using team orders? I thought they've always been very businesslike about how they approach the season. They'll give orders that help the team get the best result in the race. Things like no racing after the final stop... whatever driver is in front after the last stop finishes must not be challenged for position by the other. I'm not saying they'll do that every race, but that's the kind of decision they'll tend to make, and it more often favours the car in the most advantageous position in the race at that time, regardless of which driver is driving it. This is different to having a contracted #1 driver on which you pin your team's championship hopes, a.k.a. Ferrari.
That 1998 race, where Coulthard let Mika through, was to rectify a pitlane mixup which would have cost Mika the win, as has been mentioned. This had nothing to do with favouring Mika over David for the championship because a) it was the first race of the season, b) Mika was not clearly the better championship prospect at that time - his superiority was still to be established, and c) it was the first race after the sweeping rule changes which made the cars much narrower and introduced the grooved dry tyres, prompting McLaren (and most other teams) to discourage internal racing in an effort to be sure the cars finished the race - hence the first corner agreement. The swap manoeuvre was also simple to accomplish as both McLarens were at least 1 lap ahead of every other car on the track. Even in 1999 McLaren still let DC compete for race wins until the championship was impossible for him, and even then I'm not sure if he defered to Mika or if Mika was just faster regardless. Coulthard seems to be fast on some circuits - he's a bit of a Monaco specialist - but most of the time I doubt Mika needed team orders to help him win.