BE Spirit only stops Navigation from banishing itself from the graveyard to negate a spell/trap card.
If you want to counter Magician Navigation's special summon BE Spirit won't stop it.
You can however counter the S.Summon using the trap card Revival Gift.
With navigation you MUST S.Summon 2 monsters. Since Revival Gift will fill his field he won't S.Summon anything.
"doesn't counter Navigation, Navigation special summons one by one, not two at once."
That's the point.
Scenario: opponent has no monsters.
When your opponent activates Navi, chain it with Revival Gift to fill 2 of their monster card zones. Your opponent can only summon 1 monster.
Scenario: Opponent has 1 monster.
Your opponent's Navi can't summon anything.