The recipe I have and have been making for years for pickled green tomatoes contains a hearty amount of sliced onions. These pickles are processed in a water bath and I've never had any adverse effects.
I also have a recipe for pickled beets, via Martha Stewart, that includes onions and is also processed in a water bath.
Seems like you'd be good to go.
"As a girl I had zero interest in the stove." - Julia Child
This is real inspiration. Look what Julia became!