I know of some battlefield walk tours, but I have not heard of any travel agencies that setup military museum tours. That being said, how hard can it be to just plan to visit the museums on your own? This way you have the flexibility to spend more time at a site if needed. For example, when I went to the Bovington tank museum (before the change), I gave myself one full day. However, I ended up going back the next day because one day wasn't enough.
Also, if you want to go to the tank and car museum in Italy (Museo Storico della Motorizzazione Militare), you have to plan ahead and be prepared for on the spot changes. Because it is a restricted area, it is by appointment only, and if the group is not big enough, they tend to cancel the session.
Oh, and if you go to Rome, I highly recommend going to the Piana delle Orme history museum (Museo Storico Piana delle Orme). It is south-east of Rome (about an hour drive) just past the town of Latina. Not well know by visitors, but very much worth checking out. They even added an aircraft and boat park at the back which has about 3-4 military boats and 8-9 military aircraft. However, one day is not enough, and it is somewhat out in a rural area, but well worth a visit if you can.