Heat soak is a problem when a car has been at racing speed for a number of laps. I suspect that the desire to protect Nico's track position was indeed part of the thinking but also the Monaco pit lane has much less room to work in so having two cars in line might not have been desirable either. If I understand a couple of comments I heard, Lewis was also caught out by the Red Bull's seemingly having the opportunity to pass the safety car (and lap at speed) as it waited to pick up the leader, Rosberg.
What I really don't understand about the tyre management bit is why Nico and Lewis weren't instructed to do ball's out in-laps to pit in response to Vettel pitting. That was something Brawn and Shoemacher did almost routinely in their Ferrari days. I think Lewis has been very diplomatic about it all in taking sole blame for throwing away a podium. Nevertheless, I think he played the perfect wingman in the first stint, as the lap times were much slower than he and the car were capable of, and he helped Nico get a good lead and protected the gap. The casual viewer may not appreciate that, but behind the scenes one can be sure that "pit-lane" will. I reckon "the debt" has been paid.
Of course that's only my opinion.