Just because you can do something doesn't mean you will or should do it. Yes, intelligence probably helps with manipulation. Just like it helps you become a better murderer, yet it has nothing to do with whether someone's going to be a murderer. That's more to do with their morality, personality etc.

Manipulation per se doesn't even necessarily require high intelligence, like someone pointed out emotional manipulation that children do. Emotional manipulation is ez. Actually, in my experience, a lot of dumb people who can't do things otherwise seem to resort to manipulative tricks; intimidation, emotional abuse, lying etc..

The most intelligent people I personally know are the nicest, trustworthy people I've met. I think, since it's not mutually exclusive with empathy, sympathy, morality etc., intelligence may actually help you remain consistent and see solutions that are more in accordance to your values. Also they probably think about what their actions cause in themselves as well as others.

Something about machiavellianism (basically manipulative ppl):
"Due to their skill at interpersonal manipulation, there has often been an assumption that high Machs possess superior intelligence, or ability to understand other people in social situations. However, research has firmly established that Machiavellianism is unrelated to IQ. Furthermore, studies on emotional intelligence have found that high Machiavellianism actually tends to be associated with low emotional intelligence as assessed by both performance and questionnaire measures. Both empathy and emotion recognition have been shown to have negative correlations with Machiavellianism. Additionally, research has shown that Machiavellianism is unrelated to a more advanced theory of mind, that is, the ability to anticipate what others are thinking in social situations. If high Machs actually are skilled at manipulating others this appears to be unrelated to any special cognitive abilities as such.[2]"

So. Immoral shit is immoral shit.