i used to lower the windshield on my old CJ frequently (that was just 2 flip-clips and then down; I used to lower it at stoplights using a short rope tied to the lash hook on the inside of the windshield - actually, that is shown in my Avatar picture, sitting in "Cape traffic" on rte 3 in MA) and I lowered the windshield on my TJ (when I lived in LA) all the time.
In LA, there was something great about cruising to work on the 10 and 405 with no windshield... there are no bugs in LA, really, so that helps; it was tougher when I lived in DC. To make life easier, I always kept the forward roll cage supports OFF and stored in the garage -- that way it was only the corner windshield bolts that needed to be removed so it only took a couple minutes to drop the windshield.
The addition of that plate on the JK makes this much more complicated and annoying and increases the likelihood of scratching paint... but STILL... I'm definitely going to do it this summer.
Honestly, it's just a few bolts - it's nothing! Jeeps are meant to be toyed with! We all have the #40 Torx handy anyway!
If you have never driven your Jeep with the doors off and the windshield down, IMO you're missing out on one of the core Jeep experiences!