Option 1 is easier:

# this is the default in pd_bindings.tcl

bind all <$::modifier-Key-v>      {menu_send %W paste}

# disabled

bind all <$::modifier-Key-v>      {break}

Option 2 requires either overriding ::pd_menucommands::menu_send and intercepting the paste message or changing the paste handling in the core, I think.

Option 3: Maybe flatgui/entry shouldn't always go into edit mode (a bug) or at least have some way to control it's behavior (a feature)?