Actually after the battle fighting with Lord Harkon, Serana will tell you that she will stay at Castle Volkihar or Fort Dawnguard, but will accompany you on your travels should you ask her.

VI. > > > > Uninstall
-----------------

Before you uninstall the mod, you will want to load any games you wish to
salvage and use the RESET AFT command available in the settings menu. Or
via the Tweak Commands power. You will see a message instructing you to
save after the Reset is complete.

Once you have reset/saved any games you wish to salvage, there are two
options for uninstalling AFT:

1) Testing has shown that the easiest thing is to simply disable the mod
within the Data Files area of the startup splash.

2) If you wish to physically remove the mod, then you should disable
AFT first and startup skyrim at least 1 time while AFT is disabled.
This helps to avoid stability issues and crashing that can happen
when other mods you have installed have dependencies on AFT.

Once you have started skyrim while aft was installed but disabled,
then locate the game installation directory. Most computers will find
it in one of these two locations:

C:\Program Files\steam\steamapps\common\skyrim\

or

C:\Program Files (x86)\steam\steamapps\common\skyrim\

Delete the following files from within the skyrim directory:

(Skyrim Install)\Data\AmazingFollowerTweaks.esp
(Skyrim Install)\Data\AmazingFollowerTweaks.bsa
(Skyrim Install)\Data\AmazingFollowerTweaks.bsl