How do you see a hint at intermarriage?
Yirmiyahu is encouraging the Jewish people to keep building Klal Yisrael through marriage, even though they are in exile.
Don't despair, since eventually they'll come back to israel.
(This would seem to be in contrast to what Amram [Moshe's father] initially held, when he decided that it was better to divorce his wife than father children who would be killed by Par'oh.)
I don't see any indication of intermarriage here.
And since we known intermarriage is forbidden, and in fact Ezra worked hard at removing the foreign wives when they came back to Israel, why would we assume Yirmiyahu was encouraging it?