Deleting that folder has NO effect on Windows OS functionality, or any of it's components. The only thing that is affected is your ability to uninstall service packs. I work in a QA Test lab, and when I make all my Windows Server 2003 and Windows XP test images, I make sure this folder is deleted after all updates are performed.
I checked out that link, and the problems experienced by that user were specific to his situation and not a systemic problem of Windows XP/2003 family.
Also, since you are only removing the ability to uninstall SPs in the future by deleting this folder, then all you have to do is modify the wording for the warning dialog when checking the "Hotfix Uninstallers" checkbox, saying that this will prevent them from downgrading basically. That is the only sideffect of removing that folder.
p.s. - in short, Microsoft no longer relies on the hf_mig folder to determine what the latest version of a DLL file is when installing hotfixes. If a 3rd party software package includes an SP hotfix EXE package, the older DLL will be ignored, silently when installed if a newer one already exists.