Who knows how McLaren operate. They probably have a whole new crew for each race weekend so that 'everyone gets a turn'. 
My post was a joke, but we do know that four or five McLaren personnel left after one weekend, so it could be a small number who have stayed all year.
Whitmarsh did say they had changed their entire pit-crew for Barcelona.
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Anyway, if McLaren had left Lewis out later, his tyres would've just worn out more surely, and Alonso would've been even faster on his in-lap.
If the pit-stop had been faster, Ferrari might even have decided to have Alonso do another flying lap before pitting (unlikely), but the main problem was Alonso gained a lot of time on Hamilton by posting a fast in-lap. Looks like he learned from Barcelona, where he pushed on fresh tyres couldn't get passed Maldonaldo and ended up quite far off the lead at the end of the race. Although saving tyres then pushing on your in and out lap is a common tactic in formula one, less so nowdays because of DRS but that doesn't count in Monaco.