Do you want maps to be included within the final v1.0 release?
I dont think you need to put a server side mod together with maps, but you may create a "addon" map pack for the mod.
Rendez-vous with the first released maps !
I believe you should have 2 versions, one with and one with out. For thoes people who play on excessive servers and have no idea what it's all about and for most of them all they know is download updates have no idea about maps and such....
Some of us may just want to run quake 3 a's defalt maps for this reason, the cliant who has to download maps on dial up while waighting to enter a game...
I have been doing the best i can to inform the people about the new maps when they are on my server. This way they can be prepared for it when it happnes.
other than that i think it is a good idea to have the maps and the mod togher in one zip file.