Perhaps because I'm a native francophone, I don't find the use of masculine and feminine pronouns in the least strange .
The genders often differ between French and German (la table vs. der Tisch) but I never think of the French word when learning by heart the gender of a German noun: it would be a very silly thing to do and anyway there is no neutral in French.
That said, native francophones make quite a few mistakes: for example, even PhD holders generally believe that you should say un anagramme, whereas it is really une anagramme.
German friends have told me that their compatriots make mistakes too and that there are, moreover, regional differences: it seems that Bavarians sometimes change the gender of die Butter.
Let me remark that there are lists of nouns which have several genders (der Bonbon or das Bonbon).
Finally, it is interesting to note that some homonyms are distinguished only through their gender. For example Band
Ich habe alle bis auf den vierten (tome of a book)
Das rote steht dir gut (ribbon)
Die Beatles? Sie war die bekannteste in den sechziger Jahren (musical band)
Edit Come to think of it, there is one case in which the pronoun makes me wince:
Er war in das Mädchen sehr verliebt und küßte es ständig.
I can't say I find the usage of es here very romantic! (And I think that even some germanophones would let semantics trump syntax and say "...und küßte sie ständig". )