They'd try to fold in AIM at least a bit, but they'd ultimately conclude HYDRA is best off completely wiped out as far as how dissonant they are with the Technocracy's goals, particularly when half the organization outright worship Lovecraftian nonsense now and again and or are such. So really they're a fairly natural enemy.
Their natural enemies are more likely to be.. hah, Marvel Dracula, but they're pretty well equipped to basically end Marvel Vampires after a few years, only to get frustrated as crap seems to keep bringing them back ;p