I finally found a workaround to the problem. For some reason it does not work to create a Map Pack in Mod Buddy and just add the maps, then you get the "Invalid map file" message.
The workaround that worked for me was:
1) With Mod Buddy, create a new "Empty Mod"
2) Add a new empty folder, Maps
3) Right click on Maps and select Add -> Existing item
4) Browse to the My Games\Sid Meier's Civilization 5\Maps folder and select the map you want. Repeat for all maps you want to include in the mod
5) Build the project
6) Go to the My Games\Sid Meier's Civilization 5\MODS\<name of your mod> folder, open your .modinfo file in a texteditor.
7) Below the closing </Files> xml-tag, manually add the entry points you need, for example:
<EntryPoints>
<EntryPoint type="Map" file="Maps/SPQR_Europe_edited.Civ5Map">
<Name>My borrowed edited map</Name>
<Description>A map of Europe, North Africa, and the Middle East.</Description>
</EntryPoint>
</EntryPoints>
I haven't tried with more than one entry point, since I only needed one. It works to put the map files directly in the root folder as well. The only difference I can see with a mod created in this way and the Map Pack automatically created by Mod buddy is that the Map Pack alternative does something to the map-file, since the date-time on the file is changed to the date and time when you build the mod. When doing it manually the date-time is not changed.
I hope this workaround will work for more people.