The UFAQ for The Devil and the Dragon says that the counters are removed from Hivemind as well when you use Consume.
Virus counters on Hivemind are considered to be hosted on all other virus programs for the purposes of card effects (and can be spent as if on them).
click: Gain 2 credit for each hosted virus counter, then remove all virus counters from Consume.
I think the rationale is that the Hivemind counters are considered to be hosted on Consume (from Hivemind’s text), so when you use Consume’s click ability, “remove all virus counters from Consume” also hits the Hivemind counters (which are “considered to be hosted on” Consume).
More subtly, this means that if you were planning on using those sweet Hivemind counters to keep your Aumakua or Darwin strong, using Consume will weaken them.