There would still be diseases that would rip through the native populations, but other than that I have to think this scenario is a win for the natives.
While they had armor, medieval Europeans are going to be on a much more level playing field with the indigenous peoples, technologically. It's not out of the realm of possibility that by capturing some they could really develop their iron-working skills and within 100 years of the horse being introduced to the Great Plains you had lancers/horse archers popping up and it's not a stretch to think they would have given the Europeans fits in the New World as they did in the old.
Aside from that, you are not going to be able to send huge numbers of people over there, first why? It's not that rich in those regions the way it was in the south and the natives are mostly hostile. Once the demographic pressure in Europe is eased then it's less important. Second, you are not going to have the ease of the crossing that occurred later, could a cog make it over the ocean? Maybe but again less likely.
But also there are far fewer people in Europe anyway, so you're not going to get massive die offs+massive European settlement. By the time that starts the natives are probably going to be immune to most of the deadlier diseases and start rebuilding the population base.