How to remove permission sets from a package

It can't be done. I've had the same problem, your best bet is to start a new managed package.

However, if your App is uploaded to the AppExchange, and your a partner, you can try to contact Salesforce partner support (if your a partner and it is distributed on the AppExchange). Ask them to 'unlock' your package, you will have to have it uninstalled from all orgs where it has been installed.

PS. Oddly enough our package installed into edition that would otherwise not support permission sets, but than it wouldn't uninstall. "Uninstall Button" just disappeared and than it hung after you hit uninstall and never completely uninstalled.