I'm not sure why Apple is waiting to put the Core 2 Duo in their laptops, but it could be that they want to sell off the Core Duo laptops first. It could also be that they designed their logic board by mistake to be incompatible with Core 2 Duo chips, even though they are pin-compatible.
And yes, the CPU is soldered onto the logic board so in order to upgrade the CPU you have to replace the entire logic board. Back in the Pentium II/III days it was the norm to solder the CPU on the laptop motherboard, but today it's very rare that they do that unless they are building ultraportables in the case of the MacBook/MacBook Pro. Having the CPU soldered on means you can make the laptop thinner, but it also means you have trouble replacing parts and parts inventory can be a pain.
Apple offering CPU upgrades wouldn't make sense. But, I'm still urgently awaiting the Core 2 MacBooks...
Also, heat and "problems" won't be any worse than the Core Duo MacBook because Core 2 Duo is designed to operate in the thermal envelop of Core Duo, henceforth Core 2 doesn't consume any more power or make any more heat than Core. Basically the Core 2 is a little more powerful processor, but still works within Core architecture and Core bus speeds. When Intel releases the next version of their Core 2 Duo, it will have a new socket, new chipsets, and a faster frontside bus. This chip may well be what Apple is waiting on to upgrade the MacBook, but don't expect it until well into 2007.