Well, no doubt, just as Marie Antoinette should have been allowed to marry Wolferl Mozart and her head would've probably stayed on longer, Joseph and Eleonore's love was a fruit of its own affection, it was not provoked or forced out by political advantages. I think Maria Theresia knew of it nay, for if she did, she would have done all she could to prevent such a relationship, which was rudely against the Spanish Etiquette.
In fact, even Isabella was a sort of a relative to Joseph, since as far as I know, she was a niece to Louis XV. And for Louis XVI. was M. Antoinette's cousin, she must have been at least a distant relative to her bethroned, but alas, that was rather usual by then. All the roalty was bound into one, big family.
I am really sorry that it did never quite work out for Eleonöre and Joseph, because he then really knew no returned love, there was no tender hand to stroke his hair after a hard day of work, but I think he looked co cold and unfeeling on the outter side that everyone better avoided him, even though inside him, a very sensitive heart hid.
As for Joseph and his political views, I can of course not agree with everything, but all he has done was done with the best and most noble intentions toward his people. He was never quite understood by them, some of his reforms may have sounded needless (preventing baking of gingerbread or to embargo Castrati from singing some of Mozart's aria's not to ruin their voices), but he has all in all, published a whole 6000 of them, so I think by some of them, he may have not thought twice.
I like the way he loved his people and his country and am badly sorry for how little gratefulness he got in return for his good will. All the same, I am angry if I think how people wept after him once he died and they realised what have they lost...
A look into his soul you interested may find in this perfectly lively book: "L. Mühlbach; Joseph the Second and His Court"- the original is naturally in German, but I have an English edition from 1908 and the original title is neglected.