The quotes about Beethoven's 9th Symphony come from Susan McClary - a respected feminist musicologist.

The basic idea was that Beethoven's music has a succession of peaks - crescendos followed by falls, and has a general dramatic shape. She says this is equivalent to male preoccupation with the orgasm, which is the male dominating the female, and the only music which isn't sexist is minimalist music which doesn't have any peaks.

This argument fails on several points:
1- Women have orgasms too - some of them have them quite often and enjoy them just as much as men do, or so I am reliably informed.
2 - It is possible for a man to have an orgasm without dominating a woman in any way.
3 - There are peak experiences, mental, physical, emotional and spiritual, which are not orgasmic.

Basically the argument is that anything which builds to a point is sexist.
I assume, though I have not read the book in question, that the argument about Newton's Principia is much the same - the structure of mathematical proof does after all build up to a definite end point. Whether that is the argument or not, and whether it is a reasonable argument or not (I don't think it is, but that is open to argument), if Harding does use the phrase 'rape manual' about the Principia (and I have seen that phrase attributed to her in several places, and never seen a denial, unlike the false attributions of 'All men are rapists') then it is as crazy as it's made to sound. The Principia has nothing to do with rape, and any suggestion that it does says far more about the psyche of the person making the claim than it does about Newton.

People who make these claims do not, however, represent the majority of feminists, and it is important to keep that in mind. There are people in any group who have ridiculous extremist ideas, and it is important not to let them be the standard image one has of that group. Not all feminists are Susan McClary any more than all conservatives are Pat Robertson.