We have been in January, June and February respectively and to us the only good side of going in June was not having to worry about taking the kids out of school.
We went last year June 1-6 thinking maybe it wouldn't be too crowded yet with school just ending..........WRONG!!! Let's just compare this way, in January we did almost all of Magic Kingdom in one day with just a few things we returned to another day of the trip. In June, we didn't even do half of Magic Kingdom in a day and it was a very long day with later hours!
Plus like someone else already said it was so hot and muggy that we felt drenched by the time we walked from our room to the bus stop in the morning! It sucked the energy out of everyone in our family so much quicker. We took a swim break every day (which we didn't do in Jan.) but our swimming was often cut short by the late afternoon showers that occurred.
You will have a nice trip...you're going to Disney after all!

But just be prepared that you will not see as many things, you will have long lines and crowds and it will be hot! You have to plan on a lot of fast passes, a lot of waiting for things that don't have fast passes and a lot of people. If you are reasonable in expecting those things and don't let it frustrate you, you'll be fine.
We did have a nice trip but we definitely wouldn't choose to go back that time of year. Going just earlier this month, we actually had several cool days with highs around 60 but I would rather throw on layers and have the sun out and low crowds to enjoy Disney. As for pulling the kids out of school, they made up all their work easily and I got no complaints from teachers at all. We'd do it again that way in a heartbeat!