In a pinch I think you'll be ok. When it gets warm out try zipping it again.
Anything is better than nothing when keeping the elements out, but the velcro I think is mainly to protect the zipper from rain, snow, dirt, and salt. I wouldn't recommend cruising around too much with only velcro holding your windows on. The wind will grab them, and they aren't the cheapest things on a Jeep to replace.