First bear in mind that GregTech has a very flexible config, and any aspect of it that you do not like can most likely be disabled there.
Removing GregTech.zip from your server's mods folder will completely disable the mod and players should still be able to connect without making any changes to their client. However, their client will still expect GregTech recipes, and using default mod recipes will result in an empty slot in their crafting table's output. Clicking on this empty output slot will still craft the item, but this is guaranteed to confuse your players. This will also happen if you change server-side GregTech config, without the players changing it on their client.
The only solution to prevent this from happening, is to make sure your players use the same mods and config that your server uses.