There is nothing wrong with being unintelligent, and what you define as "unintelligent" matters a great deal when it comes to solving your "problem".
Are you talking about raw intellectual power? If so, then you're no better than Hitler. To deprive or give human rights based on how many computations you can perform in your head or how good you are at understanding scientific/mathematical/artistic concepts is barbaric. And evil. And a few other words.
Now you might be sitting there feeling very smug with yourself, thinking "well, it's OBVIOUS that I AM very intelligent" - but compared to whom? Unless you're Terence Tao, there are undoubtedly smarter people than YOU. How would you feel if someone smarter than you decided that YOU were a "lesser" person, hm? Not a nice thought is it?
I have a university degree in Biotech and I'm half way through getting my Master's degree (this time in microbiology), before moving on to my PhD. I study genetics, immunology and I perform yeast-cell assays involving the use of the Tetracycline on/off system. Can you match that? Many can, but can you? How would you like it if I decided that I was superior to YOU, just because I have a piece of paper?
I am not superior to any good citizen out there. My knowledge and intellectual skill was cultivated by my parents. Yes, some people are born with more intelligence than others. But everyone has different skill sets. Most can contribute. And those that can't due to NO FAULT OF THEIR OWN, deserve our support.
If you plan on having a society in which the "unintelligent" are weeded out, consider that some might not find you as intelligent as they are and try to weed YOU OUT. To support this sort of thing is evil, immoral and down-right DANGEROUS to you and anyone else you know.
But perhaps you aren't talking about intellectual ability - maybe you're just talking about normal people who disagree with you. In that case, they are not unintelligent. They might be ignorant, stubborn or even a little insane. And they might even be RIGHT.
I am an atheist. This was due to the fact that I was raised in many countries, in a multi-ethnic society by parents who never talked about religion. But I know many who are religious. And you know what? Many of them are intelligent, decent, hardworking people. Some are members of my family. And I love them.
It is true that there is a SLIGHT GENERAL TENDENCY towards atheism by those who are more educated or intelligent. This is, however, a TREND, not a RULE, and a very slight trend at that. Some very smart people believe in their religion, simply because they were raised to believe in it - it's an emotional issue, and they can't analyze it rationally due to the emotional and personal pain it could cause. That doesn't make them stupid.
Are you talking about political opponents? People who don't believe as you do? Well, maybe they are ignorant, or maybe (shocker here) YOU are wrong and THEY are right! Ever thought of that genius?
Are you talking about nasty people like Pat Robertson and co? Or Bin Laden? Or the gangs and drug dealers? In that case, your question is flawed - it should be about getting rid of "unintelligent people", but getting rid of "bad" people.