Why would direct control be slow? Bot controls would be the same as the character's, except for it only has 1 weapon, no traits, and no inventory... it should be FASTER to play, as you have way fewer options.
Unless you backtrack back to JHGuy for repairs. But if people are having fun, why not let them.
Especially if they grow connected to this bot. Was this your speech about roguelikes design, that adviced to give the player a companion, make the player like him, and then kill him?
Hmm, I very vividly imagined a bot menu item "Give name" :D Should be pretty cheap to implement? 8-]
Another idea, to form even stronger connection with the player through greed: what about upgrading your bots with modpacks, and maybe even utility devices? Might have its use, especially in case you have spare ones.
In case there are/will be nano-packs in the game, the bot could last very long. Can we take them down in elevators, BTW?