After yoou kill Harkon siding the Dawnguard can you use the castle?

If you sided with the Dawnguard, no. If you sided with vampires, yes.

Does the keep lock after finishing Dawnguard's main quest and siding with the Dawnguard?

If not then yes you can...most "wardrobes" and "bookcases" within the keep are safe for storage,other containers respawn after ten days with the rest of the keep.With all regular crafting amenities except a smelter within the keep, this location can be ideal for use as a home.

http://www.uesp.net/wiki/Skyrim:Volkihar_Keep