To answer OP's question, if you want to use the entire card under Windows, then go ahead and let Windows reformat it.
Of course, it won't work on the Pi anymore after this, but OP's goal is to be able to use the whole card under Windows.
Edit to add: Many people have reported that putting the card into a digital camera (if you have one) and letting the camera reformat it, will make it once again usable under Windows. I've never had occasion to test this.
Footnote: Also, there are 3rd party drivers for Windows that allow it to access (read/write) the Linux partitions. Again, I've never had occasion to test this, but I'll say that I don't trust them to get it right. It doesn't sound like a good idea to me.
GitD's list of things that are not ready for prime time:
2) 64 bit OSes
3) USB 3
Loves Linux; loves to dance.