That is a very bold claim. It's not that I'm arguing against Alonso in this case - I very much respect the guy (more so than XXX obviously and I don't intend to argue that point) - but to say Hamiltons 2nd half performance had to to with him missing Alonsos 'glorious' setup is quite a lame attempt. For one, do you honestly believe the driver is the only one in the team that can carry out the fine tuning of his car? With enough feedback (and no doubt any racer with half a brain that got into F1 can give that), there are more than enough capable technicians at McLaren to execute the wishes. To think this is solely carried and attributed to the driver... is daft.
Yes, it is a factor - but not the factor you are making it out to be. Not by a long shot.
Looking at the qualifying times I posted is far more telling to their respective performances because they are constrained to a more or less empty track with little interference and and external influence.
If you decide to look at race results though, you have a whole bunch of influences that can change the picture. Team cock-ups, rookie mistakes etc. Hamilton fucking up his tyres? Sure, his fault. Hamilton hitting the pit-stop limiter in the last race? His fault. Does Alonsons missing set-up and fine tuning bear even the slightest relevancy to these in racing occuring events? No it doesn't. Had Hamilton not made even these most basic mistakes during these races, they would be far apart in points.
I find the argument that Alonso suffered from a team not backing him up towards the end of the season far more credible and believable. If anything, M. Schumacher demonstrated how important the entire team is (driver, team, car), when battling for the championship.