Yeah, what I recommend doing is put Esuna on a gambit that is second only to Raise and your major cure spell, and then just carry remedies around with you to get rid of Disease and Doom. It works perfectly for me. Of course, this only really works if you have selected one or two members of your party to be healers, such as I have done. In fact, Ashe and Penelo, my two healers, have the exact same gambits so that they are 100% interchangable with little impact to the continuity of the party. The same is true of my Vann and Basch, and my Balthier and Fran. They are one hundred percent synonymous. Same types of weapons (though not neccessarily the exact same weapon) and same gambits. But yeah, Remedies (Lore 3 that is) and Cleanse are probably your best bet for getting rid of Disease. I've found that Vaccines are just a nuisance to carry around.