Q: Is today a good day for a DIY abortion?
This actually presents two separate, interesting issues about Juno's character. The first being the "do-it-yourself" part. Though Juno's first instinct was to have an abortion, she hardly would have considered doing anything but going to a clinic (despite her friend's comment that "heavy lifting can only help you at this point"). Not only would she probably not have known how (which brings up another issue for another day - where is the Internet in this story?), but she didn't seem to have any shame or money issues when it came to the clinic. Telling her dad was one thing, but showing up at the women's clinic was another - she wasn't like Leah's other friends who needed someone else to call for them, she was at least willing to take responsibility for herself.
And as for why she chose not to have an abortion at all, that's a little trickier. It's clear that the decision isn't motivated by religion or a committed anti-abortion stance. She would accept anyone else's decision to have an abortion, and probably help them through the process just as Leah as planning to help her. But the immediate cause of her decision was a random encounter - the girl outside the clinic mentioning fingernails, then being repelled by the image of the fingernails of the patients inside.
Of course, that pretty much implies that she had a tendency towards not wanting an abortion that was triggered by that random encounter. It was probably a combination of factors. Latent bitterness and hurt over her mother's abandonment. Having seen her stepmother pregnant with Liberty Bell. Knowing that the baby is a part of her and Bleeker. Or maybe even just an aversion to intervening in the natural order of things (hell, maybe she's read some books on Taoism), which might also explain why she still gives the baby to Vanessa even after she and Mark split up.
In any case, there are a million different reasons she could have felt wrong about having an abortion, and the movie didn't go into any of them, probably because Juno herself didn't know. She just had a bad feeling about it, and being sixteen, didn't really search her soul as to why. It'll probably come out in therapy when she's much older.
Abortion or not, that does leave the initial question: why the hell didn't Bleeker and Juno use a condom, and even stranger, why didn't anyone ask them why not? It can probably be chalked up to a combination of teenage stupidity, an adolescent feeling of immortality, the myth that you can't possibly get pregnant the first time you have sex, and being in a community that teaches only abstinence rather than safe sex. Juno isn't stupid, but she is sixteen.