TC is not likely to be the weak point for agent development in the forseeable future. There are many ways to scam/kill agents that don't rely on hacking their hosting environment.
On the other hand, I'm not aware of any "secure" chips that have stood up to inspection by FIB. Search for Tarnovsky on youtube for details. All "security features" so far are annoyances and speedbumps rather than roadblocks.
I'm not sure if a move to the main die will help or not. I think that amateurs are mostly working on small run, old fab, large feature chips. Does anyone know for sure that Intel-sized features are fundamentally beyond the reach of a FIB?
Totally agreed that the real threat will be on the software side though. For one thing, good system design should be able to prevent "Break Once, Run Everywhere" attacks, so the theoretical capability to extract keys from a TPM isn't a big deal, particularly not for distributed/networked agents.