Over the past few days I added settings to the plugin for more customization. I also fixed some bugs.
The best way to get the newest version, and to automatically stay up to date with the latest version is to use the Package Control package manager I’ve been working on. Once you manually update Alignment through Package Control, it will automatically check for and install updates whenever Sublime Text 2 starts. You can learn more at wbond.net/sublime_packages/package_control.
The newest version allows disabling indentation alignment on a per-filetype basis.
The newest version fixed that bug.