Let's get the facts straight
First of all, McLaren would not have to pay the full $100 million. The actual ruling is $100 million minus the amount the team stands to make from it's FOM (Formula One Management) yearly payout, which in this case would be in the $69 million range. So the real amount the team would have to pay is around $31 million. Yes, that's still a lot of money, but for a team that boss Ron Dennis claims "turn over roughly $450-500 million USD a year, and we are debt-free, so obviously we are a very strong company with phenomenal growth" it's really a drop in the bucket. [1]
Second, this isn't a case of some lowly McLaren employee keeping the documents at home as the team would disingenuously have the public believe. The employee in question is Mike Coughlan, chief designer of McLaren's car. According to his own testimony he showed parts of the Ferrari IP to Martin Whitmarsh, COO of McLaren, and Paddy Lowe, McLaren's engineering director. In addition, McLaren's managing director Jonathan Neale was also aware of the Ferrari documents.
[2] Coughlan also had his wife make copies of the documents at a local shop (which is how this while thing was discovered).
As to how McLaren would prove their 2008 cars don't make use of any Ferrari IP, the FIA's technical team will go over the cars -- as they do every year for every single team -- to verify no parts are the same as Ferrari's. No need for a Ferrari engineer to look at McLaren's car plans; we'll leave that to cheating teams like McLaren. ;-)
Also note that even if McLaren didn't copy a single piece of Ferrari technology, they have still gained a very significant advantage over the latter know how large the Ferrari fuel tank is, for example, or how the cars use their tyres, etc. Armed with such knowledge McLaren can (and probably did) alter their own race strategies, didn't fall prey to bluffs (that are common along the F1 pitwall), etc. To claim McLaren gained no unfair advantage over their rivals is absolutely nonsense which is why the WMSC ruled as it did.
[1] See: http://www.autosport.com/news/report.php/id/62339
[2] See: http://www.autosport.com/news/report.php/id/62303