Well I've read through this whole thread and it appears you are getting a lot of advice from a bunch of mostly emotional women, a lot of whom are maybe in the same boat as you. I thought I would give you the advice of a man for a different point of reference (chill ladies, you might be surprised).
First of all I have to say the guy is a jerk for so many reasons! You come up with this wonderful idea and he tries to horn in. Why? Because you are planning to do something that he knows your boys will enjoy and you will be making points with them while he looks bad for not thinking of it first. Secondly, he wants the benefit of being a part of the trip, but at your expense, and I don't just mean money. "We will pay the difference in the price of the room" when your part will be probably 80-90% of the cost of a slightly larger suite. How nice of his generous offer! You foot most of the bill and they get to be a part of this special "first visit to Disney" event. All of the glory and none of the "pain"......how sweet. Besides the cost, you now have to go out of your way to compromise on what you are all going to do because, after all, you don't want to be fighting and spoil the boy's first trip. You will be miserable like that!
Now, having said all of that, IF, and that's a big IF, YOU decide there is a way to compromise for the boys' sake, THEN and ONLY then should they be allowed to go. There is no way you should do it and share a room with them....PERIOD. I personally feel that the kids in a divorce suffer most if the parents can't get along afterwards and all they ever see is fussing and fighting between you both. Staying in the same room sounds like the perfect way to end up letting them see just that, especially if your EX's "second mommie" is so domineering.
The idea of telling them where and when and them making their own arrangements is the only way you should do it if YOU make that decision (after all, YOU were the one who made the decision to start with). Depending on the length of your trip you could plan some things together, and some things that are just you and your boys. They could possibly get them all to themselves one day if that is okay with you (hey, some Mommy alone time is never a bad thing and will help you to recharge and relax too).
You mentioned how much your sons like the idea of having Dad along on the trip. Were they excited about the trip BEFORE Dad invited himself??? Then I'm guessing they will still be, even if he doesn't end up going along. You came up with this idea and you made these plans. If you feel the least bit uncomfortable about them going along (and I certainly would) then don't feel guilty in the least telling him "it just ain't gonna happen."
Explain to your sons that "Daddy will take you another time, which is great because then you get two trips to Disney" and if it is all about them and not him, then he will make his own plans and take them. If it is all about him instead (and it sounds like it is to me), then you just turned the tables on the jerk for putting you on the spot about this first trip.
I personally say tell him it is just going to be a trip for three this time because truthfully I don't see any way it can work out as well for you and your boys with having to consider them in your plans too. You are going to come back home more stressed out than when you left so there goes the benefit of vacation. Trust me, you can handle it without their help and have a great time.
If you do decide to let them be a part, then as other's have said, it is only under YOUR rules and with your decisions about what you will do each day (based obviously on what your boys are excited about doing). If they can't totally agree to that, then tell them sorry, it is the only option and they will just have to take them another time. Then be firm about your decision and know you are doing the right thing all the way around.
You DO NOT and SHOULD NOT feel guilty if you decide they are not welcome on this great idea you had!
You'd need to have a REALLY friendly divorce for that to work.
).
Not all of us guys are stupid jerks (but don't tell my wife I said that....I don't want to start yet another argument in my house 
)
I was trying to be nice.... 
Yes, oh breezy one.....
. You deserve it.
