I don't consider this a bug, creating a main::isa subroutine should be harmless, &isa is only supposed to have a special meaning in OO packages. The fact that something else has decided to start calling isa() on non-OO packages is unfortunate. If you don't want Test::Deep to export &isa you can do
use Test::Deep qw(just the functions I want);
just like any other module that exports functions.