Hope it is appropriate for you to submit a feature request in a GitHub issue.
I would like it if another command similar to bundle might be implemented, however this would purge / disable all other plugins which where not explicit stated to allow that removing a "bundle" line from the users .zshrc would lead into removing / disabling the plugin without another manual action.
E.g. if a users .zshrc file changes like:
diff --git a/.zshrc b/zshrc.diff
index 004e852..45999df 100644
--- a/.zshrc
+++ b/.zshrc
@@ -23,7 +23,6 @@ antigen bundles <<EOBUNDLES
colorize
command-not-found
common-aliases
- debian
dirhistory
dot-config
emoji-clock
then antigen would remove the debian plugin automatically.