I'm... glad you asked this question. English has a strange way of taking words from other languages and punching them into shape. As with every last rule in English, there are exceptions and special cases to pronouncing French words in English.
Most of it (or so I believe) boils down to convenience. People prefer 'Parriss' instead of 'Parree' simply because the spelling has an 's' on the end, while they will happily not pronounce the 't' in 'ballet'. The only way I can attempt to shed some light on this is to go through every example you've set.
'Renaissance' is its own word in English with its own definition. In this case, you would pronounce it in an English way. Or, for someone who enjoys French, no one would mind a French pronunciation as long as it was accompanied by a heavy English accent.
'Deja vu' is a phrase we stole. 'Deja' isn't in a standard English dictionary, and neither is 'vu'. Thus, you would pronounce it as a Frenchman. 'Par excellence' is also a phrase, so a French feel is the best way to approach it.
History is slightly more difficult. I am no expert, so I'd recommend asking another teacher / historian etc for specific words. I can say with confidence though that 'Versailles' is pronounced in a very French way, as it would sound nasty in an English accent.
'Les Miserables' is part of the culture of Britannia. Everyone is aware of it. And, in English pronunciation, 'miserables' is hardly a fitting name for a show of such majesty (or so its media frenzy would suggest). Whenever culture (film, plays, books, people) is involved, chances are the pronunciation is French.
So... how to make this general. A big challenge for me. I would say: names, cultural references, words that would sound horrible in English, and phrases keep their native pronunciation; places, words we have adopted, and words that would be difficult to pronounce use English pronunciation.
The second one sounds great to me!. (As an American) I don't really ever hear people pronounce it the first way (with an 'or' sound like in "shore" and "oar"). I almost always hear it the way you pronounce it the second time, with an 'er' (like in "her" and "fur"). Another way you can pronounce it is to pronounce the u with an 'oo' sound, so it sounds like "Shoo-er" (rhymes with sewer), although this is not as common. Or at least, not in the midwest where I live. This might be a regional thing.
Best Answer
I've lived in the United States my entire life. In my experience, native speakers always pronounce these words as basicly and logicly. The pronunciation basical-ly sounds distinctly foreign; in fact, in my experience, I think that the pronunciation basical-ly is the most common pronunciation mistake that I ever hear.
In slow and careful speech, I could imagine someone saying logical-ly, but the pronunciation logicly seems more common even then.
The spellings of -al, -ly, and -ally are frustratingly inconsistent. In the following list, each word is presented as adjective - standard spelling of adverb - phonetic spelling of adverb: