名詞還是代名詞行先，有沒有準則？

In a complex sentence, the noun is normally put in the main clause and the pronoun referring to the noun is put in the subordinate clause.

So, the first sentence of your example sounds much better, being without any ambiguity.

Even if it is raised by humans, a lion will always be a wild animal.
= A lion will always be a wild animal, even if it it raised by humans. (this is a more common way to say it.)

a lion is a common noun refers to an animal.
pronoun used instead of a noun=it
Even if it is raised by humans=(dependent cl)
a lion will always be a wild animal=(main cl)
Hence alion is the subject word=a noun