Yes, it is. Find the IDs of the overmap specials you wish to remove and make a overmap_specials.json file with the following format:
[
{
"type" : "overmap_special",
"id" : "Anthill",
"copy-from" : "Anthill",
"locations" : [],
"occurrences" : [0, 0]
},{
"type" : "overmap_special",
"id" : "Acid Anthill",
"copy-from" : "Acid Anthill",
"locations" : [],
"occurrences" : [0, 0]
},{
"type" : "overmap_special",
"id" : "Bee Hive",
"copy-from" : "Bee Hive",
"locations" : [],
"occurrences" : [0, 0]
}
]