Maybe they altered Secret Invasion after the scheduling change, but nothing in it seems like it would follow on from The Marvels.
I admit that I didn't get through Secret Invasion, but I have some clues as to what happens in that series. What happens in The Marvels would fit perfectly well before SI. There's some questions that'd be raised in the other order, but given who actually picks up the refugees, maybe it is a non-issue.