Jane Goodall has received an honorary doctorate from/in Cambridge University?

NO. You receive a degree from a university, the degree is conferred by the university.
In general, you receive something from someone.

the ceremony to award degrees - graduation - may well take place IN the university.

no. From is correct.

The usual expression is "from".

"in Cambridge University" gives the impression that she got an honorary doctorate from another university while being in Cambridge University.

You can use either way. ( where did she received an honorary doctorate ? )

the known expression is "from". "in Cambridge college" supplies the consequence that she have been given an honorary doctorate from yet yet another college whilst being in Cambridge college.