I'm only familiar with the way Virtue runs Hami raids, but there, a bots/ mastermind would be part of the blue spike team. Your job would be to follow the blue targeter around and have your bots hit the designated target.
If you aren't tanking (which you probably won't be) you shouldn't be taking enough damage in a Hami raid to need Bodyguard, so I'd set the pets to Passive and manually order them to attack specific targets. The nice thing about Attack Passive is that they won't go after anything else once the chosen target dies.
As for roles, I'd say it depends on your pets. Ranged attackers like Bots, Thugs (don't summon the Bruiser until the green phase), or Mercs should probably join the Assault teams, while melee attackers might be better off helping the Scrappers kill yellows. If there's a tank shortage a MM might be able to fill in there, but I've been on a lot of blueside raids and never really seen a lack of tanks. Though if you are /Pain you might be better off healing and buffing tanks... you could even send your pets running around on Attack Passive while staying up by your tank providing heals.
Cascade, level 50 Blaster (NRG/NRG since before it was cool)
Mechmeister, level 50 Bots / Traps MM
FAR too many non-50 alts to name
[u]Arcs[u]
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Ok, just ran one of these and died quite a few times from grabbing aggro due to bots turning and shooting immediately after a mito dies. Has anyone figured out what our key role should be on blue side?