I'm actually trying not to think about how the time travel works out because it would probably eat up hours of my time, but yes, its very confusing.
I was definitely apprehensive of Lucy's idea of destroying the gate. The less time alteration that is used in this situation, the better. There has already been so much and after a while things can really get screwed up.
I also really hope this isn't going to be the end of the fighting. No one really, has shown that much forte in the battle. One thing I did notice is that, if Natsu didn't hear Lucy's plan to break the gate, then it might not be contingent upon as many of the timelines because it was an accident and not an actual attempt to change the future by destroying the gate. Just a thought.