In-universe, it makes sense that the anti-spacecraft weapons would be autonomous, since they have to be able to function at a distance; you wouldn't want the enemy to be able to jam or fake the signals from the central computers. They could have been programmed with a separate demo mode in which the central computers can override them, but apparently they weren't; this isn't too surprising, since the Minoans don't strike me as a particularly careful race.
Certainly they weren't careful enough to keep the "demo mode" for the system as a whole from getting out of control - perhaps the demonstration was activated accidentally and was never intended for use on an inhabited planet or in the vicinity of manned spacecraft, or perhaps it was intended to behave in a more restricted fashion, only operating in a designated area of the planet and not launching attacks on spacecraft. Whatever they did, it didn't work. :-)
I don't think the "offer to buy" thing is a plot loophole either, or at least not a serious one. So far as we know, the crew of the Drake were the only visitors since the disaster (there might have been a few more, but probably not too many or the problem would have been noticed earlier) and it doesn't seem unreasonable to suppose that they were all killed before they had learned enough about what was going on to make the offer.
(Note that the AI salesman would of course be programmed not to try to sell to the residents of the planet; they're the people he represents, or perhaps potential competitors, not potential buyers.)
Out-of-universe, see Valorum's answer.
