The このままで in このままでいいんだよ。 modifies the いい adverbially, meaning "It's okay to be just the way you are / just the way we are / It's okay to let it just the way it is", whereas the このままで in いかないで。このままで。 means このままでいてください or このままでいさせてください。(≒ Please stay where you are. / Please stay just as you are. / Let us be just the way we are), いてください/いさせてください being left unsaid/implied.
このままで is written in Hiragana in the modern Japanese.