HMC is a new way of making DRAM chips, not integrated memory. It could (and probably will) be added to CPUs as a separate layer of silicon, but so could the standard DRAM that we have today. The main application for HMC memory will probably be traditional DIMM sticks.
There's also no real reason that HMC would require a complete redesign of CPUs and software. It's just a bigger leap in bandwidth and power consumption than what we have seen in the transition from DDR to DDR2 and from DDR2 to DDR3, for example.