The Resolving Place Names capability is simply a tool, an assistant, a guide - and nothing more. You are not restricted to what it suggests, nor required to use it.
If you currently have England in a name and don't want it:
1) Select the name
2) Right click
3) Choose "Change the name" from right click menu
4) Erase England
5) Click ok
You're done - England is gone for that place.
You can also remove the England at the Place Name Field for a fact at the Person tab of the People Workspace. Just erase England from the place name.
You may get a screen that says you have 500 other places of that same name with England - do you want to remove England for the other 499 also? Reply yes.
Repeat one or the other of these steps for everyplace where you have England.
That said, why do that? Why not just hide it? If you hide it, you can restore England with one click. If you erase England, you can't get England back in place names without entering them all over again.
The capability at Tools > Options is for presentation purposes only. If a name of a country is entered, it will be "hidden" from view, but is still there. It is used for either hiding or showing countries in the Place Workspace or in reports.
You can also get rid of the icons about resolving at:
Tools > Options > Warnings
Uncheck: Show Unrecognized Place Name Indicators.
This will remove the icon which shows if places are resolved or not. Since you are going to remove all instances of England, all of your England places will be unresolved. You may as well just get rid of the indicator/icon.
The Place Name Authority is useful for checking spelling (but there are spelling errors in the PNA), and a rather clumsy county lookup tool - there are better ones on the web. Also, as has been said here in countless threads, is focused on the CURRENT names of places, not their historical or alternative names.