You can't have memory protection in AmigaOS. If you add the protection by isolating the applications, you will also isolate the applications from each other, making the whole thing kind of pointless.
I am not a programmer, but i think what you mean is that you cannot have full memory protection while at the same time having full compitability with old applications? If this is the case, then i think we should have a option to turn on memory protection when you dont need backwards compitability with older apps.
I dont see how new apps should suffer from this problem? Once you have a decent amount of native software this should not really be much of an issue.