RE: botnets: if the botnet operator is economically rational, then their best strategy to make money is to just follow the rules, mine coins, and then sell them on the exchanges.
RE: the original poster's question on "can somebody with lots of money and a willingness to spend it to mess with the bitcoin exchange rate and cause fear, uncertainty and doubt" :
Yes. Yes, they can. That will be true while the bitcoin economy is small, and that is why I tell people not to 'invest' money in bitcoins that they can't afford to lose.
I still predict that there will be natural price bubbles and artificial ponzi schemes and all sorts of other things causing wild swings in the value of bitcoins. Next time I talk to an economist who knows something about currency markets I'll have to ask how big a currency has to be before it is mostly immune from speculative bubbles and price manipulation...