While there is much to be said about the way the Jesuits influenced western perception of China, my own understanding of Chinese thought does not really lend credence to such a strong set of statements.

Take, for instance, the historical veracity of the figure of Confucius. There are plenty people who say that Confucius may never have existed. Since things attributed to him all date to much later than the period of his own life (excluding a handful of classics, such as the Book of Poetry which he is meant have compiled and the Spring and Autumn annals; the compilations pretty clearly only began to be contributed to him much later in the Han dynasty and Confucius' authorship of the Spring and Autumn Annals, while attributed by Mencius, is itself doubtful) it is hard to prove his existence. That having been said, he clearly wasn't invented by the Jesuits. The tradition of scholarship referencing Confucius clearly goes back to BC times and it is not hard to find primary documents from pre-Jesuit times to back that up. (Now, the Jesuits might be rightly blamed for the term "Confucianism" and by extension "Neo-Confucianism"; neither of the corresponding terms in Chinese contains 'Confucius' anywhere. That's a conversation for another time.)

Now, much more interesting is the way that the Jesuits, standing in between China and the west, spun Chinese concepts to the west and western concepts to the Chinese. As you point out, exactly how religious Chinese practice was proved a somewhat contentious issue for the Jesuits who simultaneously wanted to convince the church that the Chinese could actually be converted and convince Chinese people that they could be Christian without renouncing their own culture. Did a practice like ancestor worship violate Christianity's monotheist principles? Perhaps, but could you convince Chinese who believed in its deep importance to do without for the sake of a foreign religion? Many people, up to recent times, have spent a long time debating whether "Confucianism" is a religion or a 'philosophy' or some sort of mix or neither. Depending on what the word 'religion' means to you you will come up with different answers, but at this point, the people talking about these sorts questions don't generally cite the Jesuits. They generally look at Confucian philosophical writings, Chinese folk religion and the ways those things are or are not integrated.

I've studied early chinese history at SOAS from Andrea Janku and I must say this idea was never mentioned or given credence. It sounds very orientalist and might have stemmed from the fact that Japanese people are very derisive of Chinese culture and history and that has colored your teacher's view.

It would not however, surprise me if the Jesuits had in fact de-emphasized Chinese religion in Confucius' role, if only to avoid clashing with Christian ideas and encouraging further investment in China. He was a philosopher but that was wrapped up with religion, just as it has tended to be anywhere else. "Secularism" in particular is really a very new European trend and I doubt many Jesuits would have liked to emphasize it. More probable they simply downplayed the role of Chinese folk religion.

Personally I don't doubt that Confucius existed and traveled round the courts of the warring states. This is ancient history though, so there is very little you can say in detail about him. But as far as I know there are no good modern historians of China who give credence to the idea he was invented by Jesuits, or invented at all in fact.