Kant's contradiction in the will test suggests what you say it suggests only on the assumption that, as a rational agent, one necessarily wills one's own existence. Most human beings are happy to be alive, but it does not follow from this that any human (let alone any rational) being must will its own existence. Indeed, some philosophers have argued that, by giving birth to them, their parents violated their rights. So I think the best way to reject the Kantian argument you are suspicious about is to reject its premise that a rational being necessarily wills its own existence.
Something Kant did think rational beings necessarily will is the continued existence of rational life. Using this premise instead, we might get a moral rule against abortion when the survival of the human race hangs in the balance. Suppose rational beings found themselves in a world where, if they all took themselves to be permitted to act on the maxim to have an abortion whenever doing so promises a more pleasant life, rational life would go extinct. In that world, it would be impermissible to act on that maxim -- though a narrower maxim (e.g., "I will have an abortion if a scan reveals that my child would probably have some natural handicaps in regard to health or appearance") might still pass. In our actual world, survival of rational life is not endangered by a surplus of abortions (more likely the opposite!), so this premise does not look plausible as part of a Kantian argument against abortion.
Two more questions to think about. Suppose the permissibility of abortion did endanger the survival of the human race. And suppose we knew that there are other similarly evolved species living on other planets. Would abortion then be permissible? This question opens a possible individual-species analogy to the first paragraph above. Rational beings must will the continued existence of rational life, but not necessarily their own existence or that of their own species.
Second, what about the permissibility of sex-selective abortion when its universal permission does not threaten the survival of the human species? Are there other Kantian arguments -- related perhaps to the second formula of humanity as an end in itself -- that could support the impermissibility of aborting a fetus merely because it is female?