If the primary criteria is openness to conception rather than what is natural in the usual sense, then timing sex with the purpose of avoiding conception should be worse than the contraception that is incidental to condom use. (I'm tempted to agree here with an argument by Erasmus that celibacy and contraception are morally equivalent. 
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Maybe Thomas Aquinas didn't envision certain scenarios when developing his moral system. Haven't the Jesuits developed an approach that allows for moral principles to be weighed differently depending on the circumstances?
Aquinas did not understand NFP as practiced today since ovulation wasn't understood until the 20th Century, so when he called contraception a sin against nature, he was clearly referring to an unnatural method, which today would be similar to taking a pill or wearing a ring or condom. Think about what each means doing in a sex act: for an artificial method you have to wear something over the genitalia or take some sort of medicine. You're clearly doing something in a positive sense to have sex and not procreate. For NFP, you aren't doing something, you're not doing something. You're practicing abstinence during the fruitful periods. Otherwise, it would be a sin to have sex outside of that 72 hour period, which would also be problematic conclusion. The difference isn't something you can determine by looking at studies of the effectiveness of each in the same manner as one considers a subsidy in the political world, but rather the intrinsic nature of the act in question.
I'm not sure what you're referring to about the Jesuits, but there may be some system either I am not familiar with or am used to hearing it identified differently.
Regarding the Jesuits, I was thinking of casuist morality.
Aquinas bases his argument against contraception on the assertion that procreation is the natural end of sex. Allowance for NFP must at the very least contradict this understanding of the nature of sex, since it allows that there can be some instances of sex which do not have procreation as its proper natural end.
Procreation is the natural end of sex in general. However, there are naturally occurring circumstances where an identical sex act does not result in procreation by nature alone. Thus under those circumstances (a period of infertility) the natural end of a sex act would not be procreation, unlike the natural end of sex acts as a whole in general. St. Thomas Aquinas never addressed the idea of when sex naturally does not lead to procreation one way or another (NFP was not around in Aquinas's day but it was already known that procreation does not occur on a women's period), but he did teach that the natural law is the non-violation of natural ends. Interestingly, St. Augustine taught exactly as you say, that all sex no matter what else may be true can only be morally acceptable if it is expecting to result in procreation.
The idea of the natural end of human sexuality being procreation is a very old belief of the Church. St. Clement of Alexandria wrote against contraceptives in the 2nd Century by interpreting the Old Testament passage of Onan to say that a man's seed cannot be used in vain. Perhaps the most pointed denunciation of artificial contraceptives was St. John Chrysostym who
said:
[quote]
Why do you sow where the field is eager to destroy the fruit, where there are medicines of sterility [oral contraceptives], where there is murder before birth? You do not even let a harlot remain only a harlot, but you make her a murderess as well... Indeed, it is something worse than murder, and I do not know what to call it; for she does not kill what is formed but prevents its formation. What then? Do you condemn the gift of God and fight with his [natural] laws?... Yet such turpitude... the matter still seems indifferent to many men; even to many men having wives. In this indifference of the married men there is greater evil filth; for then poisons are prepared, not against the womb of a prostitute, but against your injured wife. Against her are these innumerable tricks. The procreation of children in marriage is the 'heritage' and 'reward' of the Lord; a blessing of God (cf. Psalm 127:3). It is the natural result of the act of sexual intercourse in marriage, which is a sacred union through which God Himself joins the two together into 'one flesh' (Genesis 1-2, Matthew 19, Mark 10, Ephesians 5, et. al.). The procreation of children is not in itself the sole purpose of marriage, but a marriage without the desire for children, and the prayer to God to bear and nurture them, is contrary to the 'sacrament of love.'
