I don't have a problem with them removing it. Roadside/highway memorials for car crash fatalities get removed, so do candles and sidewalk memorials of all sorts. Items left at the Vietnam memorial get removed. We should be happy they let ghost bikes sit as long as they do.
It seems to me the DOT did a good job balancing the scales here.
A roadside memorial like a stencil or ghost bike isn't scaring ppl away from cycling anymore than the site of a massively wrecked car on the road discourages ppl from driving. Ppl that want to try riding a bike will. Those that don't may use the possibility of what a memorial depicts as a rationalization for not riding.