The trick is finding a book from an explicitly Protestant perspective. Although this is not a period in history with which I am extensively familiar, I would doubt you'd find any modern English-language scholarship that would take such a stance. There might be older books (from the last century or two) written from Protestant viewpoints, but the trouble there is that in the field of history today few people are reading the old stuff. (In my experience, the arrogance of modern historians is the thinking that the newer work supersedes the older. Majoring in history, I was told again and again that I should not bother to cite books from even the 1960s!)
I haven't read any of the books linked below. They are apparently religiously neutral, so not quite what you're looking for, but they look solid in terms of research, etc. Maybe they'll be a good place to start. You might find the authors will cite much older sources. In those cases, look up the older books, although it might be impossible to find them still on the shelves.
Here's a couple of books on the French Wars of Religion.
http://www.amazon.com/Beneath-Cross...&sr=8-1&keywords=beneath+the+cross+diefendorf
https://www.bookdepository.com/The-French-Wars-of-Religion--1562-1629/9780521547505
This is a link to a book of primary sources from the Thirty Years' War, if you're keen on getting it right from the horse's mouth. If you're committed to serious study, primary sources are the best way to get closest to the period. The modern historical bias is limited to the selection of the documents.
http://www.amazon.com/The-Thirty-Years-War-Sourcebook/dp/0230242065
The Cambridge History of the Thirty Years' War is apparently available for free. Not a Protestant history, but Cambridge can be trusted for its scholarship.
https://www.questia.com/read/100053841/the-cambridge-modern-history
And here is a further list of sources on the French Wars of Religion.
https://www.questia.com/library/his...ilitary-interventions/french-wars-of-religion
If you can read French or German, you may be able to make use of more modern sources. However, I'd wager that modern European research is even less likely to be from a particular religious viewpoint.