This certainly is the big danger of such devastating works of satire. Unfortunately, this pamphlet was taken at face value by many during the time of its publication and Swift was indeed accused of barbarism and savagery beyond the imaginings of most people. For me, teaching this essay each year to my AP English Literature students, I normally get one student who doesn't "get" the satire and returns next class with a horrified expression on their face.
However, I believe that we can argue that Swift's irony is effective because his proposal is so exaggerated that it cannot be taken seriously. We need to remember that the success of this essay lies in the fact that Swift makes himself (overtly at least) appear like a monster to highlight the monstrous attitudes and behaviour of others, who have done nothing to help the situation that had taken the lives of so many. Thus, although there will always be the risk of those who read superficially assuming the worst, to have changed this aspect of the satire would have diluted its impact to such a great extent as to rob it of its effectiveness.