I don't grow onions but from what I have learned through growing garlic Alliums can harbour fungal diseases, some of which can remain in the soil for decades. (My friend lost 90% of her crop of 10 000 garlic this spring, from allium disease). Following a 4-year rotation reduces the chance of a build up of soil borne disease. I also make every effort to completely remove all of the little bits of alliums at harvest time and place them either in the trash or in the green bin, and no allium waste goes in my kitchen compost bucket either.
If the onions did in fact die I cannot see an issue with growing something non-allium in the same container though.